Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:35:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2022/7e3c_30979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2022/7e3c_30979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2022/7e3c_30979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2022/7e3c_30979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2022/7e3c_30979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2022/7e3c_30979.pdb" } resolution = 4.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 357": "NH1" <-> "NH2" Residue "C GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 655 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 3, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 732 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 106} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.44, per 1000 atoms: 0.83 Number of scatterers: 2937 At special positions: 0 Unit cell: (64.133, 56.524, 95.656, 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 15 16.00 O 564 8.00 N 493 7.00 C 1865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 489.6 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.962A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.880A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.456A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'C' and resid 57 through 61 removed outlier: 4.282A pdb=" N ARG C 61 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.206A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.173A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 removed outlier: 3.613A pdb=" N TYR B 79 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 59 removed outlier: 4.167A pdb=" N TYR B 33 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 96 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 97 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 92 hydrogen bonds defined for protein. 222 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: 0.74 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.52: 2204 1.52 - 1.81: 801 1.81 - 2.11: 2 2.11 - 2.40: 0 2.40 - 2.69: 1 Bond restraints: 3008 Sorted by residual: bond pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 1.332 2.695 -1.362 1.40e-02 5.10e+03 9.47e+03 bond pdb=" CA ILE B 69 " pdb=" CB ILE B 69 " ideal model delta sigma weight residual 1.551 1.530 0.020 1.08e-02 8.57e+03 3.50e+00 bond pdb=" N ARG B 71 " pdb=" CA ARG B 71 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.49e+00 bond pdb=" N HIS B 72 " pdb=" CA HIS B 72 " ideal model delta sigma weight residual 1.461 1.483 -0.022 1.20e-02 6.94e+03 3.22e+00 bond pdb=" C PRO C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.74e+00 ... (remaining 3003 not shown) Histogram of bond angle deviations from ideal: 66.92 - 84.79: 2 84.79 - 102.66: 10 102.66 - 120.54: 2800 120.54 - 138.41: 1298 138.41 - 156.28: 1 Bond angle restraints: 4111 Sorted by residual: angle pdb=" O HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 123.26 70.41 52.85 1.24e+00 6.50e-01 1.82e+03 angle pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 116.71 66.92 49.79 1.30e+00 5.92e-01 1.47e+03 angle pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 121.54 156.28 -34.74 1.91e+00 2.74e-01 3.31e+02 angle pdb=" N PRO C 59 " pdb=" CA PRO C 59 " pdb=" CB PRO C 59 " ideal model delta sigma weight residual 103.20 110.16 -6.96 9.50e-01 1.11e+00 5.37e+01 angle pdb=" N PRO B 14 " pdb=" CA PRO B 14 " pdb=" CB PRO B 14 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.87e+01 ... (remaining 4106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 1546 17.30 - 34.61: 154 34.61 - 51.91: 21 51.91 - 69.21: 5 69.21 - 86.51: 2 Dihedral angle restraints: 1728 sinusoidal: 566 harmonic: 1162 Sorted by residual: dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta harmonic sigma weight residual -180.00 -117.44 -62.56 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 148.00 -55.00 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 1725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 332 0.052 - 0.104: 96 0.104 - 0.156: 18 0.156 - 0.208: 3 0.208 - 0.260: 3 Chirality restraints: 452 Sorted by residual: chirality pdb=" CA PRO C 59 " pdb=" N PRO C 59 " pdb=" C PRO C 59 " pdb=" CB PRO C 59 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO C 8 " pdb=" N PRO C 8 " pdb=" C PRO C 8 " pdb=" CB PRO C 8 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 449 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " 0.184 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C HIS B 72 " -0.351 2.00e-02 2.50e+03 pdb=" O HIS B 72 " 0.235 2.00e-02 2.50e+03 pdb=" N ASN B 76 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 95 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " -0.019 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP B 36 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " -0.002 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 136 2.70 - 3.25: 3043 3.25 - 3.80: 4610 3.80 - 4.35: 5626 4.35 - 4.90: 9487 Nonbonded interactions: 22902 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.151 2.520 nonbonded pdb=" O LEU B 99 " pdb=" N TYR B 102 " model vdw 2.203 2.520 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP B 100 " model vdw 2.233 2.520 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 33 " model vdw 2.253 2.440 nonbonded pdb=" O ASP C 17 " pdb=" N LEU C 78 " model vdw 2.272 2.520 ... (remaining 22897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1865 2.51 5 N 493 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 6.410 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.026 1.362 3008 Z= 0.911 Angle : 1.549 52.846 4111 Z= 1.074 Chirality : 0.052 0.260 452 Planarity : 0.012 0.233 540 Dihedral : 13.812 86.511 981 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.22 % Favored : 82.28 % 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: -3.63 (0.39), residues: 395 helix: -3.32 (0.69), residues: 34 sheet: -1.46 (0.48), residues: 119 loop : -2.92 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.361 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1660 time to fit residues: 9.0552 Evaluate side-chains 40 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0010 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 3008 Z= 0.212 Angle : 0.687 10.000 4111 Z= 0.359 Chirality : 0.047 0.209 452 Planarity : 0.005 0.056 540 Dihedral : 5.900 24.257 448 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.85 % Favored : 86.90 % 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: -3.41 (0.39), residues: 397 helix: -3.06 (0.67), residues: 40 sheet: -1.37 (0.48), residues: 116 loop : -2.70 (0.37), residues: 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1326 time to fit residues: 8.7571 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 3008 Z= 0.286 Angle : 0.707 10.389 4111 Z= 0.371 Chirality : 0.048 0.220 452 Planarity : 0.006 0.085 540 Dihedral : 5.942 28.720 448 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % 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: -3.43 (0.39), residues: 397 helix: -2.95 (0.70), residues: 40 sheet: -1.39 (0.49), residues: 116 loop : -2.74 (0.36), residues: 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.389 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1345 time to fit residues: 9.0110 Evaluate side-chains 41 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.0040 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 3008 Z= 0.339 Angle : 0.729 11.134 4111 Z= 0.381 Chirality : 0.048 0.235 452 Planarity : 0.005 0.069 540 Dihedral : 5.966 24.395 448 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: -3.42 (0.38), residues: 397 helix: -3.06 (0.65), residues: 40 sheet: -1.30 (0.48), residues: 110 loop : -2.74 (0.36), residues: 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1771 time to fit residues: 11.0201 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 3008 Z= 0.260 Angle : 0.701 10.495 4111 Z= 0.367 Chirality : 0.048 0.210 452 Planarity : 0.005 0.062 540 Dihedral : 5.800 25.526 448 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.61 % Favored : 85.39 % 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: -3.35 (0.39), residues: 397 helix: -3.08 (0.64), residues: 40 sheet: -1.34 (0.48), residues: 116 loop : -2.64 (0.37), residues: 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1514 time to fit residues: 10.0147 Evaluate side-chains 44 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 3008 Z= 0.253 Angle : 0.694 10.615 4111 Z= 0.361 Chirality : 0.047 0.205 452 Planarity : 0.005 0.059 540 Dihedral : 5.634 25.613 448 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % 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: -3.31 (0.39), residues: 397 helix: -3.09 (0.62), residues: 40 sheet: -1.37 (0.47), residues: 116 loop : -2.57 (0.37), residues: 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.376 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1480 time to fit residues: 9.1803 Evaluate side-chains 41 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 3008 Z= 0.238 Angle : 0.687 8.903 4111 Z= 0.359 Chirality : 0.046 0.192 452 Planarity : 0.005 0.056 540 Dihedral : 5.676 23.708 448 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % 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: -3.23 (0.39), residues: 397 helix: -3.16 (0.58), residues: 40 sheet: -1.32 (0.47), residues: 116 loop : -2.49 (0.37), residues: 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1417 time to fit residues: 8.8629 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 3008 Z= 0.229 Angle : 0.690 8.636 4111 Z= 0.358 Chirality : 0.047 0.204 452 Planarity : 0.005 0.055 540 Dihedral : 5.588 26.369 448 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % 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: -3.19 (0.39), residues: 397 helix: -3.24 (0.55), residues: 40 sheet: -1.26 (0.48), residues: 116 loop : -2.46 (0.37), residues: 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1583 time to fit residues: 10.0622 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.0050 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3008 Z= 0.189 Angle : 0.664 8.821 4111 Z= 0.343 Chirality : 0.046 0.191 452 Planarity : 0.005 0.055 540 Dihedral : 5.449 23.676 448 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % 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: -3.10 (0.39), residues: 397 helix: -3.35 (0.62), residues: 34 sheet: -1.30 (0.47), residues: 120 loop : -2.35 (0.37), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1267 time to fit residues: 8.3007 Evaluate side-chains 40 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 3008 Z= 0.290 Angle : 0.700 9.642 4111 Z= 0.363 Chirality : 0.047 0.191 452 Planarity : 0.005 0.051 540 Dihedral : 5.681 27.537 448 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % 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: -3.17 (0.39), residues: 397 helix: -3.01 (0.63), residues: 40 sheet: -1.27 (0.48), residues: 113 loop : -2.46 (0.37), residues: 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1357 time to fit residues: 8.4271 Evaluate side-chains 39 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.052899 restraints weight = 11739.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054784 restraints weight = 7032.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056193 restraints weight = 4763.606| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3008 Z= 0.194 Angle : 0.672 9.780 4111 Z= 0.346 Chirality : 0.046 0.150 452 Planarity : 0.004 0.053 540 Dihedral : 5.520 23.810 448 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % 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: -2.98 (0.39), residues: 397 helix: -3.21 (0.65), residues: 34 sheet: -1.07 (0.48), residues: 115 loop : -2.35 (0.37), residues: 248 =============================================================================== Job complete usr+sys time: 1083.78 seconds wall clock time: 20 minutes 13.96 seconds (1213.96 seconds total)