Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 09:41:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbf_25797/04_2023/7tbf_25797.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbf_25797/04_2023/7tbf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbf_25797/04_2023/7tbf_25797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbf_25797/04_2023/7tbf_25797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbf_25797/04_2023/7tbf_25797.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbf_25797/04_2023/7tbf_25797.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 chiralities: 2 Time building chain proxies: 4.08, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 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: 0.42 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: 2.00 Time building geometry restraints manager: 2.55 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: 76.31 - 87.85: 2 87.85 - 99.38: 1 99.38 - 110.92: 2464 110.92 - 122.46: 5486 122.46 - 134.00: 1267 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: 3537 16.05 - 32.10: 363 32.10 - 48.15: 75 48.15 - 64.20: 13 64.20 - 80.25: 7 Dihedral angle restraints: 3995 sinusoidal: 1523 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 3992 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 2.520 nonbonded pdb=" N THR H 135 " pdb=" O VAL H 184 " model vdw 2.224 2.520 nonbonded pdb=" OH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASP L 60 " pdb=" N ARG L 61 " model vdw 2.247 2.520 nonbonded pdb=" OD1 ASP L 167 " pdb=" N ASP L 170 " model vdw 2.297 2.520 ... (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 ========== 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 28.990 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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: 0.010 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: 58.930 ------------------------------------------------------------------------------- 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 6779 Z= 0.528 Angle : 0.875 26.893 9220 Z= 0.469 Chirality : 0.046 0.154 1018 Planarity : 0.006 0.098 1184 Dihedral : 13.371 80.248 2391 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2457 time to fit residues: 48.4260 Evaluate side-chains 120 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0408 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 6779 Z= 0.324 Angle : 0.746 9.246 9220 Z= 0.381 Chirality : 0.046 0.197 1018 Planarity : 0.005 0.043 1184 Dihedral : 5.530 26.343 934 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.20 % Favored : 85.33 % Rotamer Outliers : 1.65 % 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: -3.30 (0.27), residues: 845 helix: -5.24 (0.24), residues: 20 sheet: -1.08 (0.30), residues: 326 loop : -2.99 (0.24), residues: 499 *********************** 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 129 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 0.834 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.2295 time to fit residues: 36.0773 Evaluate side-chains 127 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0677 time to fit residues: 2.2092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 6779 Z= 0.262 Angle : 0.695 9.272 9220 Z= 0.353 Chirality : 0.045 0.153 1018 Planarity : 0.005 0.037 1184 Dihedral : 5.276 25.774 934 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.20 % Favored : 85.33 % Rotamer Outliers : 2.20 % 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: -3.13 (0.28), residues: 845 helix: -5.21 (0.26), residues: 20 sheet: -0.90 (0.31), residues: 318 loop : -2.89 (0.25), residues: 507 *********************** 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 138 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 132 average time/residue: 0.2075 time to fit residues: 35.6946 Evaluate side-chains 121 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0684 time to fit residues: 2.1922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6779 Z= 0.214 Angle : 0.685 9.710 9220 Z= 0.344 Chirality : 0.044 0.153 1018 Planarity : 0.004 0.035 1184 Dihedral : 5.019 25.955 934 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.96 % Favored : 85.56 % Rotamer Outliers : 2.20 % 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: -2.98 (0.28), residues: 845 helix: -5.20 (0.26), residues: 20 sheet: -0.78 (0.31), residues: 322 loop : -2.81 (0.25), residues: 503 *********************** 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 139 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.801 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 133 average time/residue: 0.2004 time to fit residues: 34.8620 Evaluate side-chains 125 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0704 time to fit residues: 2.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 6779 Z= 0.292 Angle : 0.700 9.245 9220 Z= 0.355 Chirality : 0.045 0.140 1018 Planarity : 0.004 0.037 1184 Dihedral : 5.129 25.617 934 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.08 % Favored : 85.44 % Rotamer Outliers : 2.34 % 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: -2.92 (0.28), residues: 845 helix: -5.17 (0.28), residues: 20 sheet: -0.67 (0.31), residues: 316 loop : -2.80 (0.25), residues: 509 *********************** 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 133 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.781 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 126 average time/residue: 0.2058 time to fit residues: 33.7068 Evaluate side-chains 123 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0682 time to fit residues: 1.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 6779 Z= 0.230 Angle : 0.674 9.436 9220 Z= 0.340 Chirality : 0.044 0.160 1018 Planarity : 0.004 0.033 1184 Dihedral : 4.971 26.004 934 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.44 % Favored : 85.09 % Rotamer Outliers : 2.20 % 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: -5.10 (0.31), residues: 20 sheet: -0.69 (0.31), residues: 322 loop : -2.70 (0.26), residues: 503 *********************** 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 134 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.787 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 126 average time/residue: 0.2149 time to fit residues: 35.1580 Evaluate side-chains 120 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0715 time to fit residues: 2.0648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 6779 Z= 0.288 Angle : 0.709 9.685 9220 Z= 0.359 Chirality : 0.045 0.139 1018 Planarity : 0.004 0.039 1184 Dihedral : 5.091 25.476 934 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.15 % Favored : 84.38 % Rotamer Outliers : 1.51 % 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: -2.82 (0.28), residues: 845 helix: -5.09 (0.32), residues: 20 sheet: -0.60 (0.31), residues: 317 loop : -2.74 (0.25), residues: 508 *********************** 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 126 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 123 average time/residue: 0.2221 time to fit residues: 35.4110 Evaluate side-chains 117 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0662 time to fit residues: 2.0911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 62 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6779 Z= 0.181 Angle : 0.682 10.697 9220 Z= 0.337 Chirality : 0.044 0.139 1018 Planarity : 0.004 0.051 1184 Dihedral : 4.719 26.220 934 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.31 % Favored : 87.22 % Rotamer Outliers : 1.10 % 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: -2.63 (0.28), residues: 845 helix: -5.03 (0.36), residues: 20 sheet: -0.43 (0.32), residues: 303 loop : -2.58 (0.25), residues: 522 *********************** 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 123 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 118 average time/residue: 0.2392 time to fit residues: 36.1721 Evaluate side-chains 121 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0748 time to fit residues: 1.8960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 6779 Z= 0.204 Angle : 0.682 10.359 9220 Z= 0.338 Chirality : 0.044 0.138 1018 Planarity : 0.005 0.050 1184 Dihedral : 4.651 25.782 934 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.49 % Favored : 86.04 % Rotamer Outliers : 1.24 % 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: -2.53 (0.29), residues: 845 helix: -5.03 (0.36), residues: 20 sheet: -0.18 (0.32), residues: 296 loop : -2.60 (0.25), residues: 529 *********************** 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 127 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 124 average time/residue: 0.2195 time to fit residues: 35.2588 Evaluate side-chains 121 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0785 time to fit residues: 1.8965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 6779 Z= 0.311 Angle : 0.739 11.210 9220 Z= 0.371 Chirality : 0.045 0.167 1018 Planarity : 0.005 0.043 1184 Dihedral : 5.041 24.966 934 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.15 % Favored : 84.38 % Rotamer Outliers : 0.69 % 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 (0.28), residues: 845 helix: -5.03 (0.36), residues: 20 sheet: -0.24 (0.32), residues: 304 loop : -2.64 (0.25), residues: 521 ********************** 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 119 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.733 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 117 average time/residue: 0.2225 time to fit residues: 33.6136 Evaluate side-chains 115 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0811 time to fit residues: 1.2890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.092599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081616 restraints weight = 15311.689| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.73 r_work: 0.3224 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 6779 Z= 0.245 Angle : 0.714 10.523 9220 Z= 0.357 Chirality : 0.045 0.172 1018 Planarity : 0.004 0.033 1184 Dihedral : 4.914 23.892 934 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.56 % Favored : 84.97 % Rotamer Outliers : 0.83 % 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: -2.54 (0.29), residues: 845 helix: -4.97 (0.41), residues: 20 sheet: -0.34 (0.31), residues: 317 loop : -2.59 (0.26), residues: 508 =============================================================================== Job complete usr+sys time: 2001.18 seconds wall clock time: 36 minutes 56.26 seconds (2216.26 seconds total)