Starting phenix.real_space_refine on Thu Jun 5 20:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tbf_25797/06_2025/7tbf_25797.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbf_25797/06_2025/7tbf_25797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tbf_25797/06_2025/7tbf_25797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbf_25797/06_2025/7tbf_25797.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbf_25797/06_2025/7tbf_25797.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbf_25797/06_2025/7tbf_25797.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.007 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 29 5.16 5 C 4181 2.51 5 N 1114 2.21 5 O 1293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.53, per 1000 atoms: 1.14 Number of scatterers: 6617 At special positions: 0 Unit cell: (88.173, 104.76, 138.807, 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 29 16.00 O 1293 8.00 N 1114 7.00 C 4181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 20 sheets defined 2.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.529A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.524A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.532A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.695A pdb=" N TYR H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.954A pdb=" N SER H 100A" --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'H' and resid 137 through 139 Processing sheet with id=AB1, first strand: chain 'H' and resid 150 through 154 removed outlier: 3.586A pdb=" N ASN H 197 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117 removed outlier: 3.566A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER L 162 " --> pdb=" O SER L 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.628A pdb=" N LEU D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.701A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL D 50 " --> pdb=" O PHE D 34 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N HIS D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 97 " --> pdb=" O HIS D 35 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN D 39 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.605A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 85 through 86 145 hydrogen bonds defined for protein. 351 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: 1.66 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 2146 1.36 - 1.52: 3616 1.52 - 1.69: 980 1.69 - 1.85: 36 Bond restraints: 6779 Sorted by residual: bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.042 0.461 3.40e-02 8.65e+02 1.84e+02 bond pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.338 0.154 5.00e-02 4.00e+02 9.43e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.41e+00 bond pdb=" CB PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.44e+00 ... (remaining 6774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 9204 5.38 - 10.76: 13 10.76 - 16.14: 0 16.14 - 21.51: 1 21.51 - 26.89: 2 Bond angle restraints: 9220 Sorted by residual: angle pdb=" N PRO A 384 " pdb=" CD PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 103.20 76.31 26.89 1.50e+00 4.44e-01 3.21e+02 angle pdb=" CA PRO A 384 " pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 104.50 84.12 20.38 1.90e+00 2.77e-01 1.15e+02 angle pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 106.10 132.40 -26.30 3.20e+00 9.77e-02 6.76e+01 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 101.89 10.11 1.40e+00 5.10e-01 5.21e+01 angle pdb=" N ASP H 144 " pdb=" CA ASP H 144 " pdb=" C ASP H 144 " ideal model delta sigma weight residual 110.91 116.10 -5.19 1.17e+00 7.31e-01 1.97e+01 ... (remaining 9215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 3571 16.05 - 32.10: 369 32.10 - 48.15: 75 48.15 - 64.20: 15 64.20 - 80.25: 7 Dihedral angle restraints: 4037 sinusoidal: 1565 harmonic: 2472 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 150.23 -57.23 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 150.21 -57.21 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.52 56.48 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 4034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 571 0.031 - 0.062: 280 0.062 - 0.093: 99 0.093 - 0.124: 56 0.124 - 0.154: 12 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA VAL H 211 " pdb=" N VAL H 211 " pdb=" C VAL H 211 " pdb=" CB VAL H 211 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA VAL L 132 " pdb=" N VAL L 132 " pdb=" C VAL L 132 " pdb=" CB VAL L 132 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" C PRO E 40 " pdb=" CB PRO E 40 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1015 not shown) Planarity restraints: 1185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.070 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO A 384 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO A 337 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO L 15 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.023 5.00e-02 4.00e+02 ... (remaining 1182 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 62 2.63 - 3.20: 5629 3.20 - 3.77: 8740 3.77 - 4.33: 12681 4.33 - 4.90: 22334 Nonbonded interactions: 49446 Sorted by model distance: nonbonded pdb=" NE2 GLN L 124 " pdb=" O THR L 129 " model vdw 2.064 3.120 nonbonded pdb=" N THR H 135 " pdb=" O VAL H 184 " model vdw 2.224 3.120 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP L 60 " pdb=" N ARG L 61 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP L 167 " pdb=" N ASP L 170 " model vdw 2.297 3.120 ... (remaining 49441 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: 7.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.340 Find NCS groups from input model: 0.090 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: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.008 0.461 6791 Z= 0.269 Angle : 0.879 26.893 9246 Z= 0.470 Chirality : 0.046 0.154 1018 Planarity : 0.006 0.098 1184 Dihedral : 13.385 80.248 2433 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.91 % Favored : 84.62 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -3.53 (0.27), residues: 845 helix: -5.25 (0.24), residues: 20 sheet: -1.34 (0.30), residues: 316 loop : -3.03 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.009 0.003 HIS L 189 PHE 0.013 0.001 PHE A 347 TYR 0.013 0.001 TYR L 140 ARG 0.006 0.000 ARG L 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 2.48408 ( 3) link_BETA1-4 : bond 0.00975 ( 1) link_BETA1-4 : angle 2.72892 ( 3) hydrogen bonds : bond 0.30403 ( 138) hydrogen bonds : angle 9.87923 ( 351) SS BOND : bond 0.00720 ( 10) SS BOND : angle 1.61083 ( 20) covalent geometry : bond 0.00752 ( 6779) covalent geometry : angle 0.87473 ( 9220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2563 time to fit residues: 50.3999 Evaluate side-chains 120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 388 ASN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083245 restraints weight = 15112.275| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.70 r_work: 0.3241 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6791 Z= 0.167 Angle : 0.733 9.461 9246 Z= 0.373 Chirality : 0.046 0.192 1018 Planarity : 0.005 0.043 1184 Dihedral : 5.949 56.693 976 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.14 % Favored : 86.39 % Rotamer: Outliers : 1.24 % Allowed : 10.32 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -3.27 (0.27), residues: 845 helix: -5.24 (0.24), residues: 20 sheet: -1.08 (0.30), residues: 328 loop : -2.94 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.006 0.001 HIS L 189 PHE 0.012 0.001 PHE A 347 TYR 0.018 0.001 TYR D 80 ARG 0.004 0.001 ARG E 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 1) link_NAG-ASN : angle 2.18078 ( 3) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 1.86884 ( 3) hydrogen bonds : bond 0.04941 ( 138) hydrogen bonds : angle 6.71470 ( 351) SS BOND : bond 0.00681 ( 10) SS BOND : angle 1.28615 ( 20) covalent geometry : bond 0.00393 ( 6779) covalent geometry : angle 0.72937 ( 9220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8482 (mmm) cc_final: 0.7998 (pmm) REVERT: H 71 ARG cc_start: 0.8907 (ttp80) cc_final: 0.8598 (ttp80) REVERT: H 72 ASP cc_start: 0.8434 (t0) cc_final: 0.8030 (t0) REVERT: L 60 ASP cc_start: 0.8092 (t0) cc_final: 0.7871 (t0) REVERT: L 103 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8442 (tttm) REVERT: L 124 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5603 (mm-40) outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 0.2149 time to fit residues: 35.9447 Evaluate side-chains 127 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 63 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 58 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3515 r_free = 0.3515 target = 0.094174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082873 restraints weight = 15391.927| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.81 r_work: 0.3246 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6791 Z= 0.139 Angle : 0.682 9.419 9246 Z= 0.347 Chirality : 0.045 0.157 1018 Planarity : 0.004 0.040 1184 Dihedral : 5.655 56.115 976 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.90 % Favored : 86.63 % Rotamer: Outliers : 2.61 % Allowed : 11.83 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -3.09 (0.28), residues: 845 helix: -5.21 (0.25), residues: 20 sheet: -0.89 (0.30), residues: 327 loop : -2.87 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 47 HIS 0.004 0.001 HIS L 189 PHE 0.008 0.001 PHE H 146 TYR 0.016 0.001 TYR A 396 ARG 0.004 0.001 ARG E 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 2.03463 ( 3) link_BETA1-4 : bond 0.00348 ( 1) link_BETA1-4 : angle 1.68711 ( 3) hydrogen bonds : bond 0.03962 ( 138) hydrogen bonds : angle 6.04350 ( 351) SS BOND : bond 0.00621 ( 10) SS BOND : angle 1.15671 ( 20) covalent geometry : bond 0.00321 ( 6779) covalent geometry : angle 0.67915 ( 9220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: H 71 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8480 (ttp80) REVERT: H 72 ASP cc_start: 0.8403 (t0) cc_final: 0.8049 (t0) REVERT: L 60 ASP cc_start: 0.7928 (t0) cc_final: 0.7579 (t0) REVERT: L 103 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8381 (tttm) REVERT: D 90 ASP cc_start: 0.7390 (m-30) cc_final: 0.7165 (t0) REVERT: E 82 ASP cc_start: 0.8115 (m-30) cc_final: 0.7792 (m-30) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 0.1999 time to fit residues: 34.5102 Evaluate side-chains 119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN D 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080558 restraints weight = 15583.889| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.78 r_work: 0.3202 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6791 Z= 0.220 Angle : 0.741 9.301 9246 Z= 0.376 Chirality : 0.046 0.150 1018 Planarity : 0.005 0.045 1184 Dihedral : 5.906 56.676 976 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.96 % Favored : 85.56 % Rotamer: Outliers : 3.16 % Allowed : 13.76 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -3.05 (0.28), residues: 845 helix: -5.16 (0.26), residues: 20 sheet: -0.86 (0.30), residues: 331 loop : -2.86 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 47 HIS 0.009 0.002 HIS L 189 PHE 0.014 0.001 PHE L 118 TYR 0.017 0.001 TYR E 49 ARG 0.005 0.001 ARG L 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 2.35837 ( 3) link_BETA1-4 : bond 0.00532 ( 1) link_BETA1-4 : angle 1.89925 ( 3) hydrogen bonds : bond 0.04295 ( 138) hydrogen bonds : angle 5.83302 ( 351) SS BOND : bond 0.00713 ( 10) SS BOND : angle 1.21420 ( 20) covalent geometry : bond 0.00510 ( 6779) covalent geometry : angle 0.73782 ( 9220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: H 71 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8531 (ttp80) REVERT: H 72 ASP cc_start: 0.8412 (t0) cc_final: 0.8080 (t0) REVERT: H 135 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.4697 (t) REVERT: L 60 ASP cc_start: 0.7840 (t0) cc_final: 0.7441 (t0) REVERT: L 103 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8375 (tttm) REVERT: D 58 GLN cc_start: 0.9223 (mp10) cc_final: 0.8949 (mp10) outliers start: 23 outliers final: 15 residues processed: 121 average time/residue: 0.2330 time to fit residues: 36.8993 Evaluate side-chains 128 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082103 restraints weight = 15350.115| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.77 r_work: 0.3233 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6791 Z= 0.136 Angle : 0.683 9.620 9246 Z= 0.344 Chirality : 0.044 0.149 1018 Planarity : 0.004 0.041 1184 Dihedral : 5.626 56.198 976 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.90 % Favored : 86.63 % Rotamer: Outliers : 3.03 % Allowed : 15.82 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.89 (0.28), residues: 845 helix: -5.16 (0.27), residues: 20 sheet: -0.78 (0.30), residues: 324 loop : -2.69 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.004 0.001 HIS L 189 PHE 0.008 0.001 PHE H 146 TYR 0.018 0.001 TYR E 49 ARG 0.006 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 1) link_NAG-ASN : angle 2.00006 ( 3) link_BETA1-4 : bond 0.00633 ( 1) link_BETA1-4 : angle 1.73165 ( 3) hydrogen bonds : bond 0.03458 ( 138) hydrogen bonds : angle 5.61630 ( 351) SS BOND : bond 0.00664 ( 10) SS BOND : angle 1.02355 ( 20) covalent geometry : bond 0.00311 ( 6779) covalent geometry : angle 0.68035 ( 9220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: H 71 ARG cc_start: 0.8739 (ttp80) cc_final: 0.7932 (ttp80) REVERT: H 72 ASP cc_start: 0.8353 (t0) cc_final: 0.8048 (t0) REVERT: H 73 MET cc_start: 0.8534 (ttp) cc_final: 0.8230 (tpp) REVERT: L 60 ASP cc_start: 0.7806 (t0) cc_final: 0.7403 (t0) REVERT: L 103 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8416 (tttm) outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.1988 time to fit residues: 33.7622 Evaluate side-chains 126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081041 restraints weight = 15466.517| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.79 r_work: 0.3213 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6791 Z= 0.181 Angle : 0.699 9.256 9246 Z= 0.354 Chirality : 0.045 0.158 1018 Planarity : 0.005 0.044 1184 Dihedral : 5.691 56.375 976 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.44 % Favored : 85.09 % Rotamer: Outliers : 3.71 % Allowed : 16.09 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.84 (0.28), residues: 845 helix: -5.16 (0.27), residues: 20 sheet: -0.74 (0.30), residues: 327 loop : -2.67 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 47 HIS 0.006 0.001 HIS L 189 PHE 0.009 0.001 PHE H 146 TYR 0.019 0.001 TYR E 49 ARG 0.006 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 1) link_NAG-ASN : angle 2.13158 ( 3) link_BETA1-4 : bond 0.00586 ( 1) link_BETA1-4 : angle 1.83599 ( 3) hydrogen bonds : bond 0.03778 ( 138) hydrogen bonds : angle 5.58526 ( 351) SS BOND : bond 0.00664 ( 10) SS BOND : angle 1.10157 ( 20) covalent geometry : bond 0.00425 ( 6779) covalent geometry : angle 0.69590 ( 9220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8267 (mmm) cc_final: 0.7876 (pmm) REVERT: H 71 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8420 (ttp80) REVERT: H 72 ASP cc_start: 0.8361 (t0) cc_final: 0.8048 (t0) REVERT: H 135 THR cc_start: 0.6577 (OUTLIER) cc_final: 0.4683 (t) REVERT: L 60 ASP cc_start: 0.7818 (t0) cc_final: 0.7375 (t0) REVERT: L 103 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8413 (tttm) outliers start: 27 outliers final: 20 residues processed: 129 average time/residue: 0.1985 time to fit residues: 33.5028 Evaluate side-chains 132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.092236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081233 restraints weight = 15355.341| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.77 r_work: 0.3223 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6791 Z= 0.166 Angle : 0.695 9.264 9246 Z= 0.353 Chirality : 0.045 0.140 1018 Planarity : 0.004 0.043 1184 Dihedral : 5.645 56.269 976 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.25 % Favored : 86.27 % Rotamer: Outliers : 3.85 % Allowed : 16.51 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.77 (0.28), residues: 845 helix: -5.14 (0.28), residues: 20 sheet: -0.69 (0.30), residues: 327 loop : -2.63 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 148 HIS 0.005 0.001 HIS L 189 PHE 0.008 0.001 PHE H 146 TYR 0.020 0.001 TYR E 49 ARG 0.006 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 2.08162 ( 3) link_BETA1-4 : bond 0.00594 ( 1) link_BETA1-4 : angle 1.82592 ( 3) hydrogen bonds : bond 0.03593 ( 138) hydrogen bonds : angle 5.52176 ( 351) SS BOND : bond 0.00557 ( 10) SS BOND : angle 1.62124 ( 20) covalent geometry : bond 0.00386 ( 6779) covalent geometry : angle 0.68999 ( 9220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8783 (m-30) cc_final: 0.8583 (m-30) REVERT: H 2 MET cc_start: 0.8241 (mmm) cc_final: 0.7916 (pmm) REVERT: H 71 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8383 (ttp80) REVERT: H 72 ASP cc_start: 0.8387 (t0) cc_final: 0.8074 (t0) REVERT: H 135 THR cc_start: 0.6521 (OUTLIER) cc_final: 0.4743 (t) REVERT: L 60 ASP cc_start: 0.7822 (t0) cc_final: 0.7486 (t0) REVERT: L 103 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8458 (tttm) REVERT: L 124 GLN cc_start: 0.5385 (OUTLIER) cc_final: 0.5182 (mm-40) outliers start: 28 outliers final: 21 residues processed: 130 average time/residue: 0.2062 time to fit residues: 35.0670 Evaluate side-chains 132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 119 GLN Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081683 restraints weight = 15481.474| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.76 r_work: 0.3227 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6791 Z= 0.152 Angle : 0.696 9.855 9246 Z= 0.349 Chirality : 0.045 0.138 1018 Planarity : 0.004 0.043 1184 Dihedral : 5.561 56.104 976 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.25 % Favored : 86.27 % Rotamer: Outliers : 3.71 % Allowed : 17.19 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.67 (0.28), residues: 845 helix: -5.12 (0.29), residues: 20 sheet: -0.57 (0.31), residues: 323 loop : -2.59 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 148 HIS 0.004 0.001 HIS L 189 PHE 0.008 0.001 PHE H 146 TYR 0.020 0.001 TYR E 49 ARG 0.006 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 2.01800 ( 3) link_BETA1-4 : bond 0.00578 ( 1) link_BETA1-4 : angle 1.78668 ( 3) hydrogen bonds : bond 0.03536 ( 138) hydrogen bonds : angle 5.45630 ( 351) SS BOND : bond 0.00530 ( 10) SS BOND : angle 1.41610 ( 20) covalent geometry : bond 0.00354 ( 6779) covalent geometry : angle 0.69221 ( 9220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8795 (m-30) cc_final: 0.8582 (m-30) REVERT: H 2 MET cc_start: 0.8215 (mmm) cc_final: 0.7938 (pmm) REVERT: H 72 ASP cc_start: 0.8307 (t0) cc_final: 0.8015 (t0) REVERT: H 135 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.4748 (t) REVERT: L 60 ASP cc_start: 0.7827 (t0) cc_final: 0.7512 (t0) REVERT: L 103 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8460 (tttm) outliers start: 27 outliers final: 22 residues processed: 126 average time/residue: 0.2038 time to fit residues: 33.3767 Evaluate side-chains 132 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 14 optimal weight: 0.0060 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.092341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081327 restraints weight = 15610.149| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.78 r_work: 0.3218 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6791 Z= 0.171 Angle : 0.719 9.095 9246 Z= 0.362 Chirality : 0.045 0.160 1018 Planarity : 0.005 0.044 1184 Dihedral : 5.612 56.242 976 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.49 % Favored : 86.04 % Rotamer: Outliers : 3.58 % Allowed : 17.47 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.62 (0.29), residues: 845 helix: -5.12 (0.29), residues: 20 sheet: -0.52 (0.31), residues: 322 loop : -2.57 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 47 HIS 0.005 0.001 HIS L 189 PHE 0.008 0.001 PHE H 146 TYR 0.020 0.001 TYR E 49 ARG 0.009 0.001 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 1) link_NAG-ASN : angle 2.07823 ( 3) link_BETA1-4 : bond 0.00467 ( 1) link_BETA1-4 : angle 1.83871 ( 3) hydrogen bonds : bond 0.03642 ( 138) hydrogen bonds : angle 5.44099 ( 351) SS BOND : bond 0.00581 ( 10) SS BOND : angle 1.39499 ( 20) covalent geometry : bond 0.00399 ( 6779) covalent geometry : angle 0.71543 ( 9220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: H 2 MET cc_start: 0.8240 (mmm) cc_final: 0.7963 (pmm) REVERT: H 72 ASP cc_start: 0.8352 (t0) cc_final: 0.8115 (t0) REVERT: H 135 THR cc_start: 0.6515 (OUTLIER) cc_final: 0.4785 (t) REVERT: L 60 ASP cc_start: 0.7814 (t0) cc_final: 0.7515 (t0) REVERT: L 103 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8465 (tttm) outliers start: 26 outliers final: 24 residues processed: 127 average time/residue: 0.2040 time to fit residues: 33.8928 Evaluate side-chains 135 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.092077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080998 restraints weight = 15679.361| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.79 r_work: 0.3213 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6791 Z= 0.172 Angle : 0.726 11.833 9246 Z= 0.365 Chirality : 0.045 0.152 1018 Planarity : 0.005 0.044 1184 Dihedral : 5.635 56.281 976 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.85 % Favored : 85.68 % Rotamer: Outliers : 3.44 % Allowed : 17.19 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.59 (0.29), residues: 845 helix: -5.10 (0.30), residues: 20 sheet: -0.47 (0.31), residues: 321 loop : -2.57 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 148 HIS 0.005 0.001 HIS L 189 PHE 0.009 0.001 PHE H 146 TYR 0.020 0.001 TYR E 49 ARG 0.006 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 1) link_NAG-ASN : angle 2.10117 ( 3) link_BETA1-4 : bond 0.00516 ( 1) link_BETA1-4 : angle 1.85008 ( 3) hydrogen bonds : bond 0.03627 ( 138) hydrogen bonds : angle 5.41445 ( 351) SS BOND : bond 0.00578 ( 10) SS BOND : angle 1.39935 ( 20) covalent geometry : bond 0.00402 ( 6779) covalent geometry : angle 0.72270 ( 9220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1690 Ramachandran restraints generated. 845 Oldfield, 0 Emsley, 845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8329 (t0) cc_final: 0.8096 (t0) REVERT: H 135 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.4790 (t) REVERT: L 13 LEU cc_start: 0.7926 (tp) cc_final: 0.7455 (mt) REVERT: L 60 ASP cc_start: 0.7805 (t0) cc_final: 0.7500 (t0) REVERT: L 103 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8463 (tttm) REVERT: L 145 LYS cc_start: 0.7083 (tmtt) cc_final: 0.6710 (tmtt) outliers start: 25 outliers final: 24 residues processed: 127 average time/residue: 0.2161 time to fit residues: 35.8337 Evaluate side-chains 135 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 194 TYR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 189 HIS Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080877 restraints weight = 15595.286| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.78 r_work: 0.3215 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6791 Z= 0.174 Angle : 0.728 10.901 9246 Z= 0.365 Chirality : 0.045 0.151 1018 Planarity : 0.005 0.044 1184 Dihedral : 5.635 56.315 976 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.96 % Favored : 85.56 % Rotamer: Outliers : 3.58 % Allowed : 17.61 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -2.57 (0.29), residues: 845 helix: -5.10 (0.30), residues: 20 sheet: -0.43 (0.31), residues: 323 loop : -2.57 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 47 HIS 0.005 0.001 HIS L 189 PHE 0.009 0.001 PHE H 146 TYR 0.020 0.001 TYR E 49 ARG 0.006 0.001 ARG L 107 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 1) link_NAG-ASN : angle 2.11838 ( 3) link_BETA1-4 : bond 0.00565 ( 1) link_BETA1-4 : angle 1.87103 ( 3) hydrogen bonds : bond 0.03641 ( 138) hydrogen bonds : angle 5.40773 ( 351) SS BOND : bond 0.00578 ( 10) SS BOND : angle 1.38392 ( 20) covalent geometry : bond 0.00408 ( 6779) covalent geometry : angle 0.72424 ( 9220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4114.81 seconds wall clock time: 71 minutes 43.24 seconds (4303.24 seconds total)