Starting phenix.real_space_refine (version: dev) on Fri Feb 17 01:27:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/02_2023/7qeo_13935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/02_2023/7qeo_13935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/02_2023/7qeo_13935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/02_2023/7qeo_13935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/02_2023/7qeo_13935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qeo_13935/02_2023/7qeo_13935_updated.pdb" } resolution = 2.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 159": "OD1" <-> "OD2" Residue "B PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3056 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1514 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "B" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1481 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {'LMT': 2, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.28, per 1000 atoms: 0.75 Number of scatterers: 3056 At special positions: 0 Unit cell: (69.76, 66.49, 89.38, 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 28 16.00 O 502 8.00 N 481 7.00 C 2045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " 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: 1.28 Conformation dependent library (CDL) restraints added in 420.3 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 70.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 19 through 38 removed outlier: 4.275A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 100 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 158 removed outlier: 3.822A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 155 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 216 removed outlier: 4.237A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.773A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.552A pdb=" N TRP B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASP B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 46' Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 99 Proline residue: B 87 - end of helix removed outlier: 3.655A pdb=" N TYR B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG B 98 " --> pdb=" O HIS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 158 removed outlier: 3.545A pdb=" N ARG B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 216 Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 188 hydrogen bonds defined for protein. 558 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: 0.71 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 885 1.34 - 1.46: 668 1.46 - 1.57: 1539 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 3132 Sorted by residual: bond pdb=" C7 LMT A 302 " pdb=" C8 LMT A 302 " ideal model delta sigma weight residual 1.489 1.567 -0.078 2.50e-02 1.60e+03 9.66e+00 bond pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " ideal model delta sigma weight residual 1.489 1.565 -0.076 2.50e-02 1.60e+03 9.27e+00 bond pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 1.489 1.565 -0.076 2.50e-02 1.60e+03 9.27e+00 bond pdb=" C2 LMT A 301 " pdb=" C3 LMT A 301 " ideal model delta sigma weight residual 1.493 1.562 -0.069 2.30e-02 1.89e+03 9.12e+00 bond pdb=" C2 LMT B 302 " pdb=" C3 LMT B 302 " ideal model delta sigma weight residual 1.493 1.561 -0.068 2.30e-02 1.89e+03 8.84e+00 ... (remaining 3127 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.47: 73 106.47 - 113.36: 1763 113.36 - 120.25: 1149 120.25 - 127.14: 1210 127.14 - 134.03: 45 Bond angle restraints: 4240 Sorted by residual: angle pdb=" C1 LMT A 301 " pdb=" C2 LMT A 301 " pdb=" C3 LMT A 301 " ideal model delta sigma weight residual 116.40 109.60 6.80 2.18e+00 2.10e-01 9.72e+00 angle pdb=" C1 LMT B 302 " pdb=" C2 LMT B 302 " pdb=" C3 LMT B 302 " ideal model delta sigma weight residual 116.40 109.65 6.75 2.18e+00 2.10e-01 9.57e+00 angle pdb=" C ARG B 184 " pdb=" CA ARG B 184 " pdb=" CB ARG B 184 " ideal model delta sigma weight residual 111.00 108.36 2.64 8.70e-01 1.32e+00 9.18e+00 angle pdb=" N VAL B 13 " pdb=" CA VAL B 13 " pdb=" C VAL B 13 " ideal model delta sigma weight residual 112.29 110.05 2.24 9.40e-01 1.13e+00 5.68e+00 angle pdb=" C7 LMT B 302 " pdb=" C8 LMT B 302 " pdb=" C9 LMT B 302 " ideal model delta sigma weight residual 114.26 109.08 5.18 2.42e+00 1.71e-01 4.60e+00 ... (remaining 4235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 1586 14.51 - 29.01: 163 29.01 - 43.52: 47 43.52 - 58.03: 17 58.03 - 72.53: 1 Dihedral angle restraints: 1814 sinusoidal: 728 harmonic: 1086 Sorted by residual: dihedral pdb=" CA PRO B 175 " pdb=" C PRO B 175 " pdb=" N ASN B 176 " pdb=" CA ASN B 176 " ideal model delta harmonic sigma weight residual 180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO A 175 " pdb=" C PRO A 175 " pdb=" N ASN A 176 " pdb=" CA ASN A 176 " ideal model delta harmonic sigma weight residual -180.00 -160.16 -19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE A 23 " pdb=" C ILE A 23 " pdb=" N TRP A 24 " pdb=" CA TRP A 24 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 277 0.032 - 0.063: 149 0.063 - 0.095: 36 0.095 - 0.126: 18 0.126 - 0.158: 2 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA THR A 86 " pdb=" N THR A 86 " pdb=" C THR A 86 " pdb=" CB THR A 86 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA THR B 86 " pdb=" N THR B 86 " pdb=" C THR B 86 " pdb=" CB THR B 86 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA PRO B 173 " pdb=" N PRO B 173 " pdb=" C PRO B 173 " pdb=" CB PRO B 173 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 479 not shown) Planarity restraints: 504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 174 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A 175 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 174 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 175 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 133 " -0.006 2.00e-02 2.50e+03 6.53e-03 1.07e+00 pdb=" CG TRP B 133 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP B 133 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 133 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 133 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 133 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 133 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 133 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 133 " 0.000 2.00e-02 2.50e+03 ... (remaining 501 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 34 2.66 - 3.22: 2961 3.22 - 3.78: 4422 3.78 - 4.34: 5865 4.34 - 4.90: 9795 Nonbonded interactions: 23077 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 158 " model vdw 2.106 2.440 nonbonded pdb=" OH TYR A 68 " pdb=" O LYS A 168 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR B 68 " pdb=" O LYS B 168 " model vdw 2.244 2.440 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.284 2.440 nonbonded pdb=" O THR B 135 " pdb=" OG SER B 138 " model vdw 2.322 2.440 ... (remaining 23072 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 8 through 101 or resid 130 through 217 or (resid 301 and ( \ name C5 or name C6 or name C7 )) or resid 302 or (resid 303 and (name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C18 or name C19 or name C20 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C8 )))) selection = (chain 'B' and (resid 8 through 217 or resid 301 or (resid 302 and (name C4 or n \ ame C5 or name C6 or name C7 or name C8 )) or (resid 303 and (name C11 or name C \ 12 or name C13 or name C14 or name C15 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C8 )))) } 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 28 5.16 5 C 2045 2.51 5 N 481 2.21 5 O 502 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 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: 0.690 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: 1.720 Check model and map are aligned: 0.050 Process input model: 13.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.078 3132 Z= 0.520 Angle : 0.687 6.798 4240 Z= 0.361 Chirality : 0.042 0.158 482 Planarity : 0.003 0.029 504 Dihedral : 13.619 72.532 1092 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.61 (0.43), residues: 360 helix: 0.97 (0.32), residues: 241 sheet: 0.95 (1.04), residues: 22 loop : -1.00 (0.64), residues: 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 1.3081 time to fit residues: 63.1571 Evaluate side-chains 40 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8755 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 3132 Z= 0.362 Angle : 0.650 8.194 4240 Z= 0.347 Chirality : 0.044 0.150 482 Planarity : 0.004 0.031 504 Dihedral : 8.766 53.478 431 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.76 (0.44), residues: 360 helix: 1.99 (0.32), residues: 243 sheet: 1.08 (1.05), residues: 22 loop : -1.02 (0.62), residues: 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 49 average time/residue: 1.3672 time to fit residues: 68.7795 Evaluate side-chains 44 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.9746 time to fit residues: 2.5450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.8723 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3132 Z= 0.245 Angle : 0.579 7.191 4240 Z= 0.305 Chirality : 0.041 0.165 482 Planarity : 0.004 0.033 504 Dihedral : 8.296 58.784 431 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.45), residues: 360 helix: 2.39 (0.33), residues: 243 sheet: 1.29 (1.08), residues: 22 loop : -1.06 (0.62), residues: 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.416 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 1.3720 time to fit residues: 66.2263 Evaluate side-chains 46 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8746 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 3132 Z= 0.364 Angle : 0.621 6.836 4240 Z= 0.327 Chirality : 0.043 0.169 482 Planarity : 0.004 0.032 504 Dihedral : 8.254 59.063 431 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.44), residues: 360 helix: 2.36 (0.32), residues: 244 sheet: 1.28 (1.08), residues: 22 loop : -0.95 (0.62), residues: 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.359 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 1.4343 time to fit residues: 70.6605 Evaluate side-chains 47 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.9992 time to fit residues: 1.5163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8690 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3132 Z= 0.179 Angle : 0.562 7.986 4240 Z= 0.292 Chirality : 0.040 0.164 482 Planarity : 0.003 0.034 504 Dihedral : 7.479 54.274 431 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.45), residues: 360 helix: 2.66 (0.33), residues: 244 sheet: 1.58 (1.13), residues: 22 loop : -1.02 (0.63), residues: 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 1.3858 time to fit residues: 72.6513 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.2578 time to fit residues: 1.7937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8687 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 3132 Z= 0.195 Angle : 0.576 7.937 4240 Z= 0.293 Chirality : 0.040 0.155 482 Planarity : 0.003 0.031 504 Dihedral : 6.958 54.268 431 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.45), residues: 360 helix: 2.74 (0.33), residues: 244 sheet: 1.78 (1.17), residues: 22 loop : -1.02 (0.63), residues: 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 1.2341 time to fit residues: 68.5986 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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: 0.8659 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3132 Z= 0.165 Angle : 0.583 8.467 4240 Z= 0.293 Chirality : 0.038 0.152 482 Planarity : 0.003 0.032 504 Dihedral : 6.373 56.308 431 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.46), residues: 360 helix: 2.85 (0.33), residues: 243 sheet: 1.90 (1.19), residues: 22 loop : -1.03 (0.61), residues: 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 1.2632 time to fit residues: 71.3433 Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.0880 time to fit residues: 1.6154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3132 Z= 0.228 Angle : 0.623 8.444 4240 Z= 0.314 Chirality : 0.040 0.153 482 Planarity : 0.003 0.029 504 Dihedral : 6.379 59.399 431 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.46), residues: 360 helix: 2.82 (0.33), residues: 244 sheet: 1.90 (1.18), residues: 22 loop : -0.93 (0.63), residues: 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.390 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 1.3485 time to fit residues: 69.3412 Evaluate side-chains 50 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.1903 time to fit residues: 1.7049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 35 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.8662 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3132 Z= 0.182 Angle : 0.626 8.729 4240 Z= 0.313 Chirality : 0.039 0.154 482 Planarity : 0.003 0.032 504 Dihedral : 5.984 55.107 431 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.46), residues: 360 helix: 2.83 (0.33), residues: 244 sheet: 1.98 (1.20), residues: 22 loop : -0.96 (0.61), residues: 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 1.3323 time to fit residues: 68.4620 Evaluate side-chains 48 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.349 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.0170 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.8650 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3132 Z= 0.165 Angle : 0.610 8.855 4240 Z= 0.306 Chirality : 0.039 0.154 482 Planarity : 0.003 0.029 504 Dihedral : 5.616 52.096 431 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.46), residues: 360 helix: 2.89 (0.33), residues: 244 sheet: 2.11 (1.22), residues: 22 loop : -1.16 (0.60), residues: 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 3 residues processed: 49 average time/residue: 1.2696 time to fit residues: 64.0311 Evaluate side-chains 47 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.0020 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.083100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060050 restraints weight = 8421.844| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.50 r_work: 0.2821 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3132 Z= 0.171 Angle : 0.612 9.123 4240 Z= 0.309 Chirality : 0.038 0.156 482 Planarity : 0.003 0.032 504 Dihedral : 5.395 51.170 431 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.46), residues: 360 helix: 2.93 (0.33), residues: 244 sheet: 2.09 (1.21), residues: 22 loop : -1.17 (0.60), residues: 94 =============================================================================== Job complete usr+sys time: 1636.03 seconds wall clock time: 30 minutes 4.59 seconds (1804.59 seconds total)