Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:32:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/11_2022/7wp2_32667.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/11_2022/7wp2_32667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/11_2022/7wp2_32667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/11_2022/7wp2_32667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/11_2022/7wp2_32667.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wp2_32667/11_2022/7wp2_32667.pdb" } resolution = 3.52 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L ASP 34": "OD1" <-> "OD2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ASP 427": "OD1" <-> "OD2" Residue "F GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3299 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1458 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.41, per 1000 atoms: 0.73 Number of scatterers: 3299 At special positions: 0 Unit cell: (76.244, 79.356, 80.912, 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 14 16.00 O 641 8.00 N 554 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 509.2 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.905A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.037A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.520A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 89 " --> pdb=" O TYR L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.785A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.880A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER F 399 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 452 through 454 69 hydrogen bonds defined for protein. 159 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: 0.78 Time building geometry restraints manager: 1.44 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: 1049 1.34 - 1.46: 843 1.46 - 1.57: 1473 1.57 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3383 Sorted by residual: bond pdb=" C LYS F 462 " pdb=" N PRO F 463 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 3.02e+00 bond pdb=" CB CYS L 90 " pdb=" SG CYS L 90 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.85e+00 bond pdb=" C ASN L 55 " pdb=" N ARG L 56 " ideal model delta sigma weight residual 1.332 1.271 0.060 3.60e-02 7.72e+02 2.81e+00 bond pdb=" CB TYR H 114 " pdb=" CG TYR H 114 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.20e-02 2.07e+03 1.97e+00 bond pdb=" CB VAL L 60 " pdb=" CG2 VAL L 60 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 ... (remaining 3378 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 85 106.33 - 113.25: 1722 113.25 - 120.17: 1183 120.17 - 127.09: 1567 127.09 - 134.01: 37 Bond angle restraints: 4594 Sorted by residual: angle pdb=" C GLY L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" CA LEU F 387 " pdb=" CB LEU F 387 " pdb=" CG LEU F 387 " ideal model delta sigma weight residual 116.30 128.99 -12.69 3.50e+00 8.16e-02 1.31e+01 angle pdb=" C TYR F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 122.07 127.10 -5.03 1.43e+00 4.89e-01 1.24e+01 angle pdb=" C ASP F 364 " pdb=" N TYR F 365 " pdb=" CA TYR F 365 " ideal model delta sigma weight residual 121.54 127.45 -5.91 1.91e+00 2.74e-01 9.58e+00 angle pdb=" C SER H 52 " pdb=" N PHE H 53 " pdb=" CA PHE H 53 " ideal model delta sigma weight residual 120.44 124.43 -3.99 1.30e+00 5.92e-01 9.40e+00 ... (remaining 4589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1753 17.78 - 35.55: 171 35.55 - 53.33: 25 53.33 - 71.11: 3 71.11 - 88.88: 3 Dihedral angle restraints: 1955 sinusoidal: 750 harmonic: 1205 Sorted by residual: dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PHE F 338 " pdb=" C PHE F 338 " pdb=" N GLY F 339 " pdb=" CA GLY F 339 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE F 472 " pdb=" C ILE F 472 " pdb=" N TYR F 473 " pdb=" CA TYR F 473 " ideal model delta harmonic sigma weight residual 180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 1952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 309 0.047 - 0.094: 135 0.094 - 0.141: 33 0.141 - 0.188: 7 0.188 - 0.235: 5 Chirality restraints: 489 Sorted by residual: chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB THR H 91 " pdb=" CA THR H 91 " pdb=" OG1 THR H 91 " pdb=" CG2 THR H 91 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL H 100 " pdb=" CA VAL H 100 " pdb=" CG1 VAL H 100 " pdb=" CG2 VAL H 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 486 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 498 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO F 499 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO F 499 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 499 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 13 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO L 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO F 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 909 2.79 - 3.32: 2630 3.32 - 3.85: 5262 3.85 - 4.37: 5959 4.37 - 4.90: 10778 Nonbonded interactions: 25538 Sorted by model distance: nonbonded pdb=" OH TYR L 93 " pdb=" OD1 ASP H 113 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR F 415 " pdb=" OD1 ASP F 420 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR L 51 " pdb=" O THR F 415 " model vdw 2.280 2.440 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.288 2.520 ... (remaining 25533 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 14 5.16 5 C 2090 2.51 5 N 554 2.21 5 O 641 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=0.00 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: 7.250 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: 38.230 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 15.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 3383 Z= 0.437 Angle : 0.900 12.687 4594 Z= 0.499 Chirality : 0.056 0.235 489 Planarity : 0.007 0.070 594 Dihedral : 13.752 88.882 1195 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer Outliers : 0.28 % 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: -4.60 (0.34), residues: 416 helix: -5.07 (0.26), residues: 20 sheet: -2.60 (0.38), residues: 162 loop : -3.28 (0.31), residues: 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.403 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1880 time to fit residues: 17.2698 Evaluate side-chains 60 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0340 time to fit residues: 0.6064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 39 GLN H 84 ASN F 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 3383 Z= 0.275 Angle : 0.607 7.913 4594 Z= 0.317 Chirality : 0.044 0.139 489 Planarity : 0.005 0.047 594 Dihedral : 5.894 51.116 485 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 1.70 % 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: -4.01 (0.35), residues: 416 helix: -4.79 (0.45), residues: 20 sheet: -2.14 (0.42), residues: 140 loop : -2.91 (0.32), residues: 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.407 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1722 time to fit residues: 13.1538 Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0351 time to fit residues: 0.8634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.0030 chunk 40 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3383 Z= 0.214 Angle : 0.559 7.561 4594 Z= 0.290 Chirality : 0.042 0.138 489 Planarity : 0.004 0.038 594 Dihedral : 5.477 48.351 485 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 3.12 % 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: -3.78 (0.36), residues: 416 helix: -4.70 (0.52), residues: 20 sheet: -1.82 (0.41), residues: 148 loop : -2.87 (0.33), residues: 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.409 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 65 average time/residue: 0.1520 time to fit residues: 12.1855 Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0347 time to fit residues: 0.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3383 Z= 0.221 Angle : 0.569 7.691 4594 Z= 0.291 Chirality : 0.043 0.137 489 Planarity : 0.004 0.034 594 Dihedral : 5.256 45.004 485 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer Outliers : 3.12 % 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: -3.49 (0.37), residues: 416 helix: -4.67 (0.55), residues: 20 sheet: -1.58 (0.42), residues: 150 loop : -2.68 (0.34), residues: 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.308 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 67 average time/residue: 0.1394 time to fit residues: 11.4763 Evaluate side-chains 57 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.295 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0282 time to fit residues: 0.5896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 0.0020 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.0020 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3383 Z= 0.187 Angle : 0.548 6.886 4594 Z= 0.280 Chirality : 0.043 0.139 489 Planarity : 0.004 0.034 594 Dihedral : 4.992 41.406 485 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 1.99 % 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: -3.29 (0.38), residues: 416 helix: -4.68 (0.54), residues: 20 sheet: -1.44 (0.41), residues: 165 loop : -2.57 (0.35), residues: 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.405 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.1647 time to fit residues: 12.0948 Evaluate side-chains 57 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0344 time to fit residues: 0.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 3383 Z= 0.387 Angle : 0.672 8.811 4594 Z= 0.344 Chirality : 0.046 0.149 489 Planarity : 0.004 0.034 594 Dihedral : 5.533 42.004 485 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer Outliers : 1.42 % 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: -3.39 (0.38), residues: 416 helix: -4.75 (0.46), residues: 20 sheet: -1.51 (0.41), residues: 161 loop : -2.63 (0.35), residues: 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.381 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 0.1414 time to fit residues: 9.9957 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0346 time to fit residues: 0.6067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 3383 Z= 0.391 Angle : 0.675 8.418 4594 Z= 0.345 Chirality : 0.046 0.149 489 Planarity : 0.004 0.036 594 Dihedral : 5.655 43.609 485 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 0.85 % 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: 416 helix: -4.81 (0.40), residues: 20 sheet: -1.55 (0.42), residues: 161 loop : -2.62 (0.35), residues: 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.381 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.1547 time to fit residues: 10.9777 Evaluate side-chains 58 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0347 time to fit residues: 0.6359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0040 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN F 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3383 Z= 0.194 Angle : 0.583 7.380 4594 Z= 0.297 Chirality : 0.043 0.175 489 Planarity : 0.004 0.043 594 Dihedral : 5.152 40.562 485 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 1.42 % 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: -3.12 (0.38), residues: 416 helix: -4.76 (0.41), residues: 20 sheet: -1.41 (0.44), residues: 146 loop : -2.32 (0.35), residues: 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.423 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 0.1612 time to fit residues: 11.6760 Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0367 time to fit residues: 0.6758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0000 chunk 33 optimal weight: 0.0670 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3383 Z= 0.216 Angle : 0.577 7.208 4594 Z= 0.293 Chirality : 0.044 0.180 489 Planarity : 0.004 0.037 594 Dihedral : 5.039 37.777 485 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 0.85 % 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: -2.97 (0.38), residues: 416 helix: -4.63 (0.48), residues: 20 sheet: -1.33 (0.44), residues: 146 loop : -2.21 (0.35), residues: 250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.407 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 56 average time/residue: 0.1650 time to fit residues: 11.2703 Evaluate side-chains 55 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0325 time to fit residues: 0.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8277 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 3383 Z= 0.344 Angle : 0.646 7.582 4594 Z= 0.330 Chirality : 0.045 0.173 489 Planarity : 0.004 0.034 594 Dihedral : 5.365 38.624 485 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.57 % 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: -3.05 (0.38), residues: 416 helix: -4.68 (0.43), residues: 20 sheet: -1.41 (0.44), residues: 146 loop : -2.24 (0.35), residues: 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.392 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 0.1899 time to fit residues: 12.4809 Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0415 time to fit residues: 0.6794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.151929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135056 restraints weight = 4600.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138180 restraints weight = 2551.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140277 restraints weight = 1711.967| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3383 Z= 0.225 Angle : 0.577 7.061 4594 Z= 0.296 Chirality : 0.043 0.172 489 Planarity : 0.004 0.033 594 Dihedral : 5.114 36.903 485 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 0.28 % 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: -2.92 (0.38), residues: 416 helix: -4.54 (0.52), residues: 20 sheet: -1.36 (0.44), residues: 146 loop : -2.13 (0.35), residues: 250 =============================================================================== Job complete usr+sys time: 1577.90 seconds wall clock time: 29 minutes 39.57 seconds (1779.57 seconds total)