Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 16:39:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/04_2023/7nll_12465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/04_2023/7nll_12465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/04_2023/7nll_12465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/04_2023/7nll_12465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/04_2023/7nll_12465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nll_12465/04_2023/7nll_12465_updated.pdb" } resolution = 2.89 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= 0.078 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2915 atoms to isotropic. 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 22 5.16 5 C 3220 2.51 5 N 829 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5056 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1501 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1494 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1012 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.64 Number of scatterers: 5056 At special positions: 0 Unit cell: (92.92, 57.57, 105.04, 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 22 16.00 O 985 8.00 N 829 7.00 C 3220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 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 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 785.2 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 8 sheets defined 10.4% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 384 through 387 No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 384 through 387 No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.329A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 409' Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing sheet with id= A, first strand: chain 'B' and resid 354 through 358 Processing sheet with id= B, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= C, first strand: chain 'D' and resid 354 through 358 Processing sheet with id= D, first strand: chain 'D' and resid 452 through 454 Processing sheet with id= E, first strand: chain 'A' and resid 3 through 7 Processing sheet with id= F, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.595A pdb=" N SER A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG A 38 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.595A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 318 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: 1.28 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1620 1.34 - 1.46: 1413 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 5196 Sorted by residual: bond pdb=" C5 RTV D1001 " pdb=" O5 RTV D1001 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C5 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.411 1.435 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C1 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C2 RTV B1001 " pdb=" C3 RTV B1001 " ideal model delta sigma weight residual 1.547 1.525 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C4 RTV B1001 " pdb=" C5 RTV B1001 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 5191 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.46: 173 107.46 - 114.09: 2722 114.09 - 120.72: 2177 120.72 - 127.35: 1958 127.35 - 133.99: 52 Bond angle restraints: 7082 Sorted by residual: angle pdb=" N TYR C 109 " pdb=" CA TYR C 109 " pdb=" C TYR C 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.09e+00 angle pdb=" N TYR A 109 " pdb=" CA TYR A 109 " pdb=" C TYR A 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.08e+00 angle pdb=" CA TYR B 369 " pdb=" CB TYR B 369 " pdb=" CG TYR B 369 " ideal model delta sigma weight residual 113.90 116.98 -3.08 1.80e+00 3.09e-01 2.93e+00 angle pdb=" CA TYR D 369 " pdb=" CB TYR D 369 " pdb=" CG TYR D 369 " ideal model delta sigma weight residual 113.90 116.95 -3.05 1.80e+00 3.09e-01 2.87e+00 angle pdb=" N ASP A 119 " pdb=" CA ASP A 119 " pdb=" C ASP A 119 " ideal model delta sigma weight residual 111.36 113.10 -1.74 1.09e+00 8.42e-01 2.54e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 2749 15.77 - 31.54: 194 31.54 - 47.30: 37 47.30 - 63.07: 6 63.07 - 78.84: 2 Dihedral angle restraints: 2988 sinusoidal: 1100 harmonic: 1888 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.02 35.98 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA ARG D 408 " pdb=" CB ARG D 408 " pdb=" CG ARG D 408 " pdb=" CD ARG D 408 " ideal model delta sinusoidal sigma weight residual -180.00 -131.61 -48.39 3 1.50e+01 4.44e-03 8.63e+00 ... (remaining 2985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 745 1.000 - 2.000: 0 2.000 - 3.001: 0 3.001 - 4.001: 0 4.001 - 5.001: 2 Chirality restraints: 747 Sorted by residual: chirality pdb=" C2 RTV D1001 " pdb=" C1 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" N2 RTV D1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" C2 RTV B1001 " pdb=" C1 RTV B1001 " pdb=" C3 RTV B1001 " pdb=" N2 RTV B1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 744 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 116 " 0.010 2.00e-02 2.50e+03 7.11e-03 1.27e+00 pdb=" CG TRP C 116 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP C 116 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 116 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " -0.010 2.00e-02 2.50e+03 6.98e-03 1.22e+00 pdb=" CG TRP A 116 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 109 " -0.006 2.00e-02 2.50e+03 6.69e-03 8.94e-01 pdb=" CG TYR C 109 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 109 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 109 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 109 " 0.001 2.00e-02 2.50e+03 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1066 2.78 - 3.31: 4472 3.31 - 3.84: 8618 3.84 - 4.37: 10549 4.37 - 4.90: 17846 Nonbonded interactions: 42551 Sorted by model distance: nonbonded pdb=" ND2 ASN B 343 " pdb=" O7 RTV B1001 " model vdw 2.255 2.520 nonbonded pdb=" N GLY C 15 " pdb=" O LEU C 86 " model vdw 2.557 2.520 nonbonded pdb=" N GLY A 15 " pdb=" O LEU A 86 " model vdw 2.557 2.520 nonbonded pdb=" N GLN C 13 " pdb=" OE1 GLN C 13 " model vdw 2.571 2.520 nonbonded pdb=" N GLN A 13 " pdb=" OE1 GLN A 13 " model vdw 2.572 2.520 ... (remaining 42546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 133) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 333 through 381 or (resid 382 and (name N or name CA or na \ me C or name O or name CB )) or resid 383 through 527 or resid 1001)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.003 0.028 5196 Z= 0.184 Angle : 0.549 4.419 7082 Z= 0.304 Chirality : 0.263 5.001 747 Planarity : 0.004 0.023 927 Dihedral : 10.855 78.842 1774 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 648 helix: -0.59 (0.84), residues: 36 sheet: 2.74 (0.37), residues: 164 loop : 0.35 (0.27), residues: 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.9790 time to fit residues: 167.1506 Evaluate side-chains 115 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 501 ASN D 394 ASN A 74 ASN C 3 GLN C 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 5196 Z= 0.355 Angle : 0.594 6.448 7082 Z= 0.319 Chirality : 0.047 0.164 747 Planarity : 0.004 0.041 927 Dihedral : 4.526 15.877 730 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 4.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.32), residues: 648 helix: -1.43 (0.89), residues: 30 sheet: 1.26 (0.37), residues: 201 loop : 0.13 (0.29), residues: 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.601 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 134 average time/residue: 0.7823 time to fit residues: 111.2795 Evaluate side-chains 123 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.4376 time to fit residues: 3.1740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 ASN A 74 ASN A 82 GLN ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 5196 Z= 0.247 Angle : 0.529 8.231 7082 Z= 0.278 Chirality : 0.043 0.141 747 Planarity : 0.004 0.037 927 Dihedral : 4.249 14.570 730 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 4.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 648 helix: -1.54 (1.00), residues: 24 sheet: 1.59 (0.37), residues: 177 loop : -0.17 (0.27), residues: 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.575 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 0.7700 time to fit residues: 108.1735 Evaluate side-chains 125 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.3700 time to fit residues: 3.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 0.3980 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 7.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 5196 Z= 0.331 Angle : 0.570 9.240 7082 Z= 0.299 Chirality : 0.044 0.180 747 Planarity : 0.004 0.040 927 Dihedral : 4.460 15.649 730 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 6.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.31), residues: 648 helix: -1.61 (0.83), residues: 30 sheet: 1.17 (0.37), residues: 177 loop : -0.23 (0.28), residues: 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 119 time to evaluate : 0.600 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 136 average time/residue: 0.7282 time to fit residues: 105.5681 Evaluate side-chains 137 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 11 residues processed: 13 average time/residue: 0.3759 time to fit residues: 6.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.0570 chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 15 optimal weight: 0.0770 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5196 Z= 0.169 Angle : 0.552 10.954 7082 Z= 0.286 Chirality : 0.043 0.207 747 Planarity : 0.004 0.047 927 Dihedral : 4.211 19.773 730 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.54 % Favored : 98.30 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 648 helix: -2.11 (0.87), residues: 24 sheet: 1.33 (0.37), residues: 167 loop : -0.31 (0.27), residues: 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 0.651 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 131 average time/residue: 0.7541 time to fit residues: 105.1292 Evaluate side-chains 132 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.2846 time to fit residues: 3.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 59 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 5196 Z= 0.242 Angle : 0.566 11.569 7082 Z= 0.292 Chirality : 0.044 0.186 747 Planarity : 0.004 0.043 927 Dihedral : 4.298 23.223 730 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 5.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.30), residues: 648 helix: -2.21 (0.84), residues: 24 sheet: 1.16 (0.37), residues: 167 loop : -0.39 (0.27), residues: 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 130 average time/residue: 0.7925 time to fit residues: 109.4184 Evaluate side-chains 136 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 9 average time/residue: 0.2878 time to fit residues: 3.7790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 61 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.3120 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5196 Z= 0.146 Angle : 0.524 10.674 7082 Z= 0.269 Chirality : 0.042 0.153 747 Planarity : 0.004 0.044 927 Dihedral : 4.019 25.029 730 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 4.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 648 helix: -1.87 (0.99), residues: 18 sheet: 1.17 (0.37), residues: 167 loop : -0.36 (0.27), residues: 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 131 average time/residue: 0.7886 time to fit residues: 109.4984 Evaluate side-chains 127 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 5 average time/residue: 0.0919 time to fit residues: 1.4187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 5196 Z= 0.452 Angle : 0.651 12.873 7082 Z= 0.340 Chirality : 0.047 0.218 747 Planarity : 0.004 0.045 927 Dihedral : 4.793 23.182 730 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.60 % Rotamer Outliers : 5.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.31), residues: 648 helix: -2.27 (0.90), residues: 24 sheet: 0.58 (0.36), residues: 179 loop : -0.45 (0.28), residues: 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 0.591 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 127 average time/residue: 0.8208 time to fit residues: 110.5104 Evaluate side-chains 131 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 10 average time/residue: 0.0937 time to fit residues: 2.1443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 409 GLN D 481 ASN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5196 Z= 0.199 Angle : 0.556 9.273 7082 Z= 0.289 Chirality : 0.043 0.165 747 Planarity : 0.004 0.046 927 Dihedral : 4.372 25.720 730 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.70 % Favored : 98.15 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.31), residues: 648 helix: -2.61 (0.98), residues: 18 sheet: 0.55 (0.36), residues: 179 loop : -0.48 (0.27), residues: 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.7937 time to fit residues: 107.0218 Evaluate side-chains 127 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.4086 time to fit residues: 2.9977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5196 Z= 0.251 Angle : 0.572 9.608 7082 Z= 0.296 Chirality : 0.044 0.165 747 Planarity : 0.004 0.045 927 Dihedral : 4.396 25.043 730 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.60 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.31), residues: 648 helix: -2.66 (0.97), residues: 18 sheet: 0.47 (0.36), residues: 179 loop : -0.48 (0.28), residues: 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.7812 time to fit residues: 98.8110 Evaluate side-chains 124 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.1162 time to fit residues: 1.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.099512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.084469 restraints weight = 8647.566| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.80 r_work: 0.3057 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 5196 Z= 0.159 Angle : 0.570 17.251 7082 Z= 0.280 Chirality : 0.042 0.149 747 Planarity : 0.004 0.046 927 Dihedral : 4.118 25.406 730 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.16 % Favored : 97.69 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 648 helix: -2.61 (0.98), residues: 18 sheet: 0.71 (0.37), residues: 169 loop : -0.49 (0.27), residues: 461 =============================================================================== Job complete usr+sys time: 2124.28 seconds wall clock time: 38 minutes 24.52 seconds (2304.52 seconds total)