Starting phenix.real_space_refine on Mon Sep 23 15:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/09_2024/8ve1_43161.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/09_2024/8ve1_43161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/09_2024/8ve1_43161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/09_2024/8ve1_43161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/09_2024/8ve1_43161.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve1_43161/09_2024/8ve1_43161.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 8 5.16 5 C 2331 2.51 5 N 592 2.21 5 O 725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3656 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 901 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 894 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 2.85, per 1000 atoms: 0.78 Number of scatterers: 3656 At special positions: 0 Unit cell: (80.366, 65.754, 54.514, 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 8 16.00 O 725 8.00 N 592 7.00 C 2331 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 447.7 milliseconds 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 7 sheets defined 7.7% alpha, 59.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.625A pdb=" N TYR A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.787A pdb=" N TYR B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.656A pdb=" N TYR C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.526A pdb=" N SER A 23 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 23 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.551A pdb=" N VAL B 14 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 5.407A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N GLU A 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA B 91 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL A 94 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 24 removed outlier: 3.594A pdb=" N SER C 23 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 23 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 23 through 24 removed outlier: 3.594A pdb=" N SER C 23 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 14 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.634A pdb=" N VAL C 32 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 46 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 30 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 41 through 48 removed outlier: 6.671A pdb=" N VAL D 32 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER D 46 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 30 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 618 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: 1.06 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 598 1.31 - 1.43: 1027 1.43 - 1.56: 2087 1.56 - 1.68: 2 1.68 - 1.81: 12 Bond restraints: 3726 Sorted by residual: bond pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 1.461 1.568 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" CAH 1WZ B 201 " pdb=" CAR 1WZ B 201 " ideal model delta sigma weight residual 1.461 1.567 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" CAV 1WZ B 201 " pdb=" NAW 1WZ B 201 " ideal model delta sigma weight residual 1.376 1.471 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" CAV 1WZ C 201 " pdb=" NAW 1WZ C 201 " ideal model delta sigma weight residual 1.376 1.470 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C LYS C 15 " pdb=" O LYS C 15 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.19e-02 7.06e+03 2.14e+01 ... (remaining 3721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 5025 2.13 - 4.26: 57 4.26 - 6.40: 1 6.40 - 8.53: 3 8.53 - 10.66: 2 Bond angle restraints: 5088 Sorted by residual: angle pdb=" CAH 1WZ B 201 " pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 126.24 115.58 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " ideal model delta sigma weight residual 114.10 107.17 6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CAH 1WZ C 201 " pdb=" CAI 1WZ C 201 " pdb=" CAS 1WZ C 201 " ideal model delta sigma weight residual 126.24 116.87 9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" CAI 1WZ C 201 " pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 126.51 118.59 7.92 3.00e+00 1.11e-01 6.98e+00 angle pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 114.10 109.12 4.98 2.00e+00 2.50e-01 6.19e+00 ... (remaining 5083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 1952 15.63 - 31.26: 164 31.26 - 46.88: 39 46.88 - 62.51: 9 62.51 - 78.14: 4 Dihedral angle restraints: 2168 sinusoidal: 810 harmonic: 1358 Sorted by residual: dihedral pdb=" CA ALA C 91 " pdb=" C ALA C 91 " pdb=" N GLU C 92 " pdb=" CA GLU C 92 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " pdb=" CE LYS B 15 " ideal model delta sinusoidal sigma weight residual 60.00 116.93 -56.93 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CG LYS A 80 " pdb=" CD LYS A 80 " pdb=" CE LYS A 80 " pdb=" NZ LYS A 80 " ideal model delta sinusoidal sigma weight residual -180.00 -127.10 -52.90 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 2165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 285 0.024 - 0.048: 159 0.048 - 0.071: 60 0.071 - 0.095: 9 0.095 - 0.119: 60 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 570 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 112 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO D 113 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 92 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.20e+00 pdb=" CD GLU C 92 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLU C 92 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU C 92 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 112 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.35e-01 pdb=" N PRO C 113 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO C 113 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 113 " -0.013 5.00e-02 4.00e+02 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 764 2.79 - 3.31: 3079 3.31 - 3.84: 6216 3.84 - 4.37: 7383 4.37 - 4.90: 13199 Nonbonded interactions: 30641 Sorted by model distance: nonbonded pdb=" O HIS A 90 " pdb=" O HOH A 201 " model vdw 2.258 3.040 nonbonded pdb=" OG SER C 52 " pdb=" OE1 GLU C 54 " model vdw 2.312 3.040 nonbonded pdb=" O ASN C 27 " pdb=" O HOH C 301 " model vdw 2.318 3.040 nonbonded pdb=" O HIS B 88 " pdb=" O HOH B 301 " model vdw 2.335 3.040 nonbonded pdb=" NH1 ARG D 34 " pdb=" OE2 GLU D 42 " model vdw 2.337 3.120 ... (remaining 30636 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 124)) selection = (chain 'B' and (resid 10 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 124)) selection = (chain 'C' and (resid 10 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 91 or (resid 92 and (name N or nam \ e CA or name C or name O or name CB )) or resid 93 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 124)) selection = (chain 'D' and (resid 10 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 through 91 or (resid 92 and (name N or nam \ e CA or name C or name O or name CB )) or resid 93 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 124)) } 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: 0.750 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.190 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 3726 Z= 0.381 Angle : 0.583 10.659 5088 Z= 0.278 Chirality : 0.046 0.119 573 Planarity : 0.003 0.029 648 Dihedral : 13.153 78.141 1292 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.39), residues: 458 helix: -0.53 (0.80), residues: 34 sheet: 1.33 (0.32), residues: 239 loop : -0.64 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 41 HIS 0.001 0.000 HIS B 56 PHE 0.014 0.001 PHE C 64 TYR 0.010 0.001 TYR D 116 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.404 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 1.3757 time to fit residues: 117.2064 Evaluate side-chains 74 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3726 Z= 0.389 Angle : 0.613 5.976 5088 Z= 0.328 Chirality : 0.051 0.158 573 Planarity : 0.004 0.033 648 Dihedral : 6.548 70.697 504 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.60 % Allowed : 10.68 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.37), residues: 458 helix: -0.44 (0.76), residues: 35 sheet: 1.26 (0.31), residues: 231 loop : -1.14 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 41 HIS 0.003 0.001 HIS B 88 PHE 0.012 0.002 PHE C 64 TYR 0.013 0.002 TYR D 116 ARG 0.003 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.420 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 1.5013 time to fit residues: 126.1463 Evaluate side-chains 81 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3726 Z= 0.215 Angle : 0.564 9.778 5088 Z= 0.288 Chirality : 0.048 0.144 573 Planarity : 0.004 0.031 648 Dihedral : 6.557 61.415 504 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.60 % Allowed : 13.80 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.36), residues: 458 helix: -0.32 (0.74), residues: 37 sheet: 0.93 (0.30), residues: 231 loop : -1.05 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 41 HIS 0.002 0.000 HIS B 88 PHE 0.008 0.001 PHE A 33 TYR 0.012 0.001 TYR D 116 ARG 0.002 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7498 (mptp) outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 1.4778 time to fit residues: 128.7092 Evaluate side-chains 85 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3726 Z= 0.281 Angle : 0.574 7.284 5088 Z= 0.296 Chirality : 0.048 0.150 573 Planarity : 0.004 0.031 648 Dihedral : 6.566 64.962 504 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.60 % Allowed : 16.93 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.35), residues: 458 helix: -0.14 (0.76), residues: 35 sheet: 0.73 (0.30), residues: 232 loop : -1.13 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 41 HIS 0.002 0.000 HIS B 88 PHE 0.009 0.001 PHE A 33 TYR 0.012 0.002 TYR D 116 ARG 0.004 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7496 (mptp) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 1.5894 time to fit residues: 133.3679 Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 3726 Z= 0.386 Angle : 0.620 6.495 5088 Z= 0.320 Chirality : 0.050 0.154 573 Planarity : 0.004 0.033 648 Dihedral : 6.845 62.360 504 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.65 % Allowed : 15.36 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.35), residues: 458 helix: -0.25 (0.75), residues: 35 sheet: 0.60 (0.30), residues: 231 loop : -1.28 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 41 HIS 0.003 0.001 HIS B 88 PHE 0.011 0.002 PHE A 33 TYR 0.012 0.002 TYR D 116 ARG 0.003 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7497 (mptp) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 1.5582 time to fit residues: 130.7924 Evaluate side-chains 87 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 98 ASN B 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3726 Z= 0.283 Angle : 0.576 7.698 5088 Z= 0.296 Chirality : 0.049 0.149 573 Planarity : 0.004 0.033 648 Dihedral : 7.100 86.483 504 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.86 % Allowed : 16.93 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.35), residues: 458 helix: -0.33 (0.74), residues: 37 sheet: 0.56 (0.31), residues: 220 loop : -1.18 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 41 HIS 0.004 0.001 HIS A 56 PHE 0.009 0.001 PHE A 33 TYR 0.012 0.002 TYR D 116 ARG 0.003 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7506 (mptp) REVERT: C 60 THR cc_start: 0.8434 (t) cc_final: 0.8065 (m) REVERT: D 54 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7297 (pm20) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 1.5286 time to fit residues: 133.0371 Evaluate side-chains 92 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3726 Z= 0.232 Angle : 0.551 6.170 5088 Z= 0.288 Chirality : 0.048 0.145 573 Planarity : 0.004 0.032 648 Dihedral : 6.652 72.033 504 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.34 % Allowed : 18.23 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.36), residues: 458 helix: -0.18 (0.76), residues: 37 sheet: 0.57 (0.31), residues: 220 loop : -1.10 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 41 HIS 0.002 0.000 HIS B 88 PHE 0.008 0.001 PHE A 33 TYR 0.012 0.001 TYR D 116 ARG 0.003 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7463 (mptp) REVERT: D 54 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7164 (pm20) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 1.5230 time to fit residues: 129.3796 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN D 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3726 Z= 0.248 Angle : 0.561 5.821 5088 Z= 0.294 Chirality : 0.049 0.146 573 Planarity : 0.004 0.032 648 Dihedral : 6.329 59.528 504 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.12 % Allowed : 17.97 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.36), residues: 458 helix: -0.21 (0.75), residues: 37 sheet: 0.56 (0.31), residues: 220 loop : -1.09 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 41 HIS 0.002 0.000 HIS B 88 PHE 0.008 0.001 PHE A 33 TYR 0.012 0.001 TYR D 116 ARG 0.003 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7464 (mptp) REVERT: D 54 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7166 (pm20) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 1.4476 time to fit residues: 124.5870 Evaluate side-chains 87 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 98 ASN B 98 ASN D 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3726 Z= 0.241 Angle : 0.556 5.688 5088 Z= 0.291 Chirality : 0.048 0.146 573 Planarity : 0.004 0.032 648 Dihedral : 6.019 60.105 504 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.86 % Allowed : 17.97 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.35), residues: 458 helix: -0.18 (0.76), residues: 37 sheet: 0.60 (0.32), residues: 216 loop : -1.05 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 41 HIS 0.003 0.001 HIS A 56 PHE 0.008 0.001 PHE A 33 TYR 0.012 0.001 TYR D 116 ARG 0.004 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7461 (mptp) REVERT: D 54 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7170 (pm20) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 1.4719 time to fit residues: 125.1406 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN D 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3726 Z= 0.146 Angle : 0.497 4.423 5088 Z= 0.263 Chirality : 0.047 0.139 573 Planarity : 0.003 0.031 648 Dihedral : 5.621 67.679 504 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.86 % Allowed : 18.49 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.36), residues: 458 helix: 0.15 (0.79), residues: 37 sheet: 0.55 (0.32), residues: 212 loop : -0.91 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 41 HIS 0.001 0.000 HIS B 88 PHE 0.007 0.001 PHE D 44 TYR 0.013 0.001 TYR C 116 ARG 0.004 0.000 ARG D 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8087 (t0) cc_final: 0.7877 (p0) REVERT: D 54 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7203 (pm20) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 1.3827 time to fit residues: 127.7334 Evaluate side-chains 87 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 54 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 124 ASN D 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117415 restraints weight = 4262.345| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.05 r_work: 0.3249 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3726 Z= 0.227 Angle : 0.583 5.766 5088 Z= 0.306 Chirality : 0.048 0.145 573 Planarity : 0.004 0.030 648 Dihedral : 5.865 65.491 504 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.82 % Allowed : 19.79 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.35), residues: 458 helix: 0.02 (0.78), residues: 37 sheet: 0.76 (0.31), residues: 214 loop : -1.04 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 41 HIS 0.002 0.000 HIS B 88 PHE 0.008 0.001 PHE A 33 TYR 0.012 0.001 TYR D 116 ARG 0.004 0.001 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2399.98 seconds wall clock time: 42 minutes 21.29 seconds (2541.29 seconds total)