Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:44:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/11_2022/7ey4_31377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/11_2022/7ey4_31377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/11_2022/7ey4_31377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/11_2022/7ey4_31377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/11_2022/7ey4_31377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey4_31377/11_2022/7ey4_31377.pdb" } resolution = 3.69 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= -0.000 sd= 0.023 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 405": "OD1" <-> "OD2" Residue "R GLU 471": "OE1" <-> "OE2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4683 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 985 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.17, per 1000 atoms: 0.68 Number of scatterers: 4683 At special positions: 0 Unit cell: (62.13, 80.66, 110.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 894 8.00 N 772 7.00 C 3000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.05 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN N 165 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 716.7 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 11 sheets defined 7.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.648A pdb=" N ASP H 31 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.577A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 3.653A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.923A pdb=" N GLU L 70 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.193A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.513A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 45 through 47 removed outlier: 4.277A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG H 98 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.668A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.687A pdb=" N ILE R 402 " --> pdb=" O TYR R 508 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 4.174A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 252 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: 1.51 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1473 1.35 - 1.48: 1418 1.48 - 1.61: 1891 1.61 - 1.74: 0 1.74 - 1.88: 21 Bond restraints: 4803 Sorted by residual: bond pdb=" CA SER H 107 " pdb=" CB SER H 107 " ideal model delta sigma weight residual 1.532 1.464 0.067 1.82e-02 3.02e+03 1.37e+01 bond pdb=" N CYS N 166 " pdb=" CA CYS N 166 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.58e+00 bond pdb=" N PHE N 168 " pdb=" CA PHE N 168 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.22e-02 6.72e+03 7.54e+00 bond pdb=" CA SER H 104 " pdb=" CB SER H 104 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.22e-02 6.72e+03 7.34e+00 bond pdb=" N ASP H 105 " pdb=" CA ASP H 105 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.04e+00 ... (remaining 4798 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.68: 117 106.68 - 113.53: 2453 113.53 - 120.38: 1840 120.38 - 127.23: 2064 127.23 - 134.08: 45 Bond angle restraints: 6519 Sorted by residual: angle pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 109.64 105.50 4.14 5.38e-01 3.45e+00 5.91e+01 angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 111.90 107.22 4.68 8.10e-01 1.52e+00 3.34e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 127.53 -13.13 2.30e+00 1.89e-01 3.26e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.18 -12.78 2.30e+00 1.89e-01 3.09e+01 angle pdb=" N CYS R 379 " pdb=" CA CYS R 379 " pdb=" C CYS R 379 " ideal model delta sigma weight residual 108.38 114.13 -5.75 1.35e+00 5.49e-01 1.82e+01 ... (remaining 6514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.54: 2538 18.54 - 37.08: 186 37.08 - 55.62: 42 55.62 - 74.16: 7 74.16 - 92.70: 6 Dihedral angle restraints: 2779 sinusoidal: 1090 harmonic: 1689 Sorted by residual: dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 132.41 47.59 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -10.28 -75.72 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CA CYS R 379 " pdb=" C CYS R 379 " pdb=" N TYR R 380 " pdb=" CA TYR R 380 " ideal model delta harmonic sigma weight residual -180.00 -140.32 -39.68 0 5.00e+00 4.00e-02 6.30e+01 ... (remaining 2776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 625 0.078 - 0.156: 70 0.156 - 0.233: 3 0.233 - 0.311: 2 0.311 - 0.389: 1 Chirality restraints: 701 Sorted by residual: chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.79e+02 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.58e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 698 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.322 2.00e-02 2.50e+03 2.72e-01 9.26e+02 pdb=" C7 NAG A 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.471 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.293 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG A 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.430 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO L 8 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.035 5.00e-02 4.00e+02 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 180 2.70 - 3.25: 4472 3.25 - 3.80: 6731 3.80 - 4.35: 8835 4.35 - 4.90: 15297 Nonbonded interactions: 35515 Sorted by model distance: nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.150 2.440 nonbonded pdb=" OD1 ASP N 40 " pdb=" OH TYR N 204 " model vdw 2.203 2.440 nonbonded pdb=" OH TYR N 91 " pdb=" OE1 GLU N 191 " model vdw 2.217 2.440 nonbonded pdb=" NH2 ARG H 98 " pdb=" OD2 ASP H 117 " model vdw 2.237 2.520 nonbonded pdb=" NH2 ARG L 31 " pdb=" OE1 GLU R 340 " model vdw 2.241 2.520 ... (remaining 35510 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3000 2.51 5 N 772 2.21 5 O 894 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 13.160 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 18.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.007 0.068 4803 Z= 0.444 Angle : 0.885 13.127 6519 Z= 0.525 Chirality : 0.052 0.389 701 Planarity : 0.014 0.272 835 Dihedral : 14.080 92.702 1689 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.50 % Favored : 86.15 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.36 % 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 (0.34), residues: 563 helix: -3.57 (0.84), residues: 20 sheet: -0.83 (0.39), residues: 181 loop : -2.14 (0.31), residues: 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.495 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2112 time to fit residues: 32.2279 Evaluate side-chains 98 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 ASN N 164 ASN N 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4803 Z= 0.248 Angle : 0.702 8.456 6519 Z= 0.374 Chirality : 0.049 0.386 701 Planarity : 0.005 0.057 835 Dihedral : 8.519 101.736 669 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.95 % Favored : 89.88 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.16 (0.34), residues: 563 helix: -3.54 (0.90), residues: 20 sheet: -0.27 (0.39), residues: 188 loop : -2.08 (0.31), residues: 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.576 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 116 average time/residue: 0.2004 time to fit residues: 28.5409 Evaluate side-chains 97 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0470 time to fit residues: 1.2657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 4803 Z= 0.256 Angle : 0.679 9.087 6519 Z= 0.356 Chirality : 0.047 0.297 701 Planarity : 0.005 0.058 835 Dihedral : 8.194 100.430 669 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.24 % Favored : 90.59 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.07 (0.34), residues: 563 helix: -3.47 (0.89), residues: 20 sheet: -0.21 (0.39), residues: 187 loop : -2.01 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.516 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.1999 time to fit residues: 24.2253 Evaluate side-chains 91 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0447 time to fit residues: 1.2337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.0030 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN N 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 4803 Z= 0.268 Angle : 0.655 7.538 6519 Z= 0.347 Chirality : 0.046 0.272 701 Planarity : 0.005 0.091 835 Dihedral : 8.080 101.075 669 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.59 % Favored : 90.23 % Rotamer Outliers : 4.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.34), residues: 563 helix: -3.25 (0.92), residues: 20 sheet: -0.05 (0.39), residues: 187 loop : -2.02 (0.31), residues: 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.582 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 109 average time/residue: 0.2020 time to fit residues: 27.1665 Evaluate side-chains 99 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0512 time to fit residues: 1.8759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.0470 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN N 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 4803 Z= 0.280 Angle : 0.669 7.936 6519 Z= 0.354 Chirality : 0.046 0.251 701 Planarity : 0.005 0.087 835 Dihedral : 8.074 101.431 669 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.35), residues: 563 helix: -3.11 (0.92), residues: 20 sheet: -0.11 (0.38), residues: 202 loop : -2.02 (0.32), residues: 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.574 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 99 average time/residue: 0.2048 time to fit residues: 24.8358 Evaluate side-chains 93 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0540 time to fit residues: 1.0325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 4803 Z= 0.248 Angle : 0.706 18.070 6519 Z= 0.366 Chirality : 0.046 0.229 701 Planarity : 0.005 0.094 835 Dihedral : 8.026 102.076 669 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.35), residues: 563 helix: -3.02 (0.95), residues: 20 sheet: -0.07 (0.37), residues: 207 loop : -1.94 (0.32), residues: 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.526 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 108 average time/residue: 0.1875 time to fit residues: 25.3065 Evaluate side-chains 97 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0447 time to fit residues: 1.3464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0270 chunk 45 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN N 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 4803 Z= 0.187 Angle : 0.674 17.274 6519 Z= 0.349 Chirality : 0.046 0.308 701 Planarity : 0.005 0.093 835 Dihedral : 7.898 103.270 669 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.35), residues: 563 helix: -2.89 (1.00), residues: 20 sheet: 0.30 (0.38), residues: 201 loop : -1.90 (0.32), residues: 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.558 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 98 average time/residue: 0.1963 time to fit residues: 23.9193 Evaluate side-chains 93 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0615 time to fit residues: 1.2589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.0000 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN R 334 ASN R 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 4803 Z= 0.210 Angle : 0.667 15.853 6519 Z= 0.347 Chirality : 0.045 0.270 701 Planarity : 0.005 0.097 835 Dihedral : 7.814 103.449 669 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.35), residues: 563 helix: -2.76 (1.03), residues: 20 sheet: 0.36 (0.38), residues: 201 loop : -1.82 (0.32), residues: 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.557 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.1923 time to fit residues: 22.9649 Evaluate side-chains 98 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0467 time to fit residues: 1.3600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 4803 Z= 0.293 Angle : 0.718 15.526 6519 Z= 0.375 Chirality : 0.047 0.267 701 Planarity : 0.006 0.102 835 Dihedral : 7.994 103.327 669 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.35), residues: 563 helix: -3.24 (0.79), residues: 26 sheet: 0.09 (0.37), residues: 202 loop : -1.87 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.563 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 95 average time/residue: 0.2107 time to fit residues: 24.6664 Evaluate side-chains 96 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0570 time to fit residues: 1.0261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 4803 Z= 0.266 Angle : 0.708 14.972 6519 Z= 0.370 Chirality : 0.046 0.257 701 Planarity : 0.006 0.095 835 Dihedral : 7.929 103.484 669 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.35), residues: 563 helix: -3.27 (0.80), residues: 26 sheet: 0.12 (0.37), residues: 202 loop : -1.85 (0.33), residues: 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.562 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 98 average time/residue: 0.1929 time to fit residues: 23.5917 Evaluate side-chains 96 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0470 time to fit residues: 1.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 chunk 1 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112038 restraints weight = 6535.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114113 restraints weight = 5064.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115436 restraints weight = 4252.814| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 4803 Z= 0.215 Angle : 0.687 13.983 6519 Z= 0.359 Chirality : 0.046 0.246 701 Planarity : 0.006 0.102 835 Dihedral : 7.952 103.869 669 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.35), residues: 563 helix: -3.24 (0.81), residues: 26 sheet: 0.29 (0.38), residues: 206 loop : -1.84 (0.33), residues: 331 =============================================================================== Job complete usr+sys time: 1455.99 seconds wall clock time: 26 minutes 53.94 seconds (1613.94 seconds total)