Starting phenix.real_space_refine (version: dev) on Sun Dec 11 18:52:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/12_2022/6nf6_9361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/12_2022/6nf6_9361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/12_2022/6nf6_9361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/12_2022/6nf6_9361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/12_2022/6nf6_9361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/12_2022/6nf6_9361_updated.pdb" } resolution = 3.32 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= 1.000 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 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 161": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 6598 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3264 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 5 Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3264 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 12, 'TRANS': 398} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.53, per 1000 atoms: 0.69 Number of scatterers: 6598 At special positions: 0 Unit cell: (91.67, 75.19, 75.19, 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 48 16.00 O 1098 8.00 N 1024 7.00 C 4428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 50 through 77 Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'A' and resid 128 through 151 Processing helix chain 'A' and resid 163 through 181 removed outlier: 3.724A pdb=" N HIS A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 214 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.820A pdb=" N GLU A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 279 Proline residue: A 261 - end of helix removed outlier: 3.824A pdb=" N THR A 264 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 327 Processing helix chain 'A' and resid 335 through 364 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 376 through 404 removed outlier: 4.212A pdb=" N GLY A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 436 removed outlier: 3.589A pdb=" N LEU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 511 Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 529 through 558 Proline residue: A 541 - end of helix Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 84 through 108 Processing helix chain 'B' and resid 128 through 151 Processing helix chain 'B' and resid 163 through 181 removed outlier: 3.724A pdb=" N HIS B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 214 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.820A pdb=" N GLU B 223 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 279 Proline residue: B 261 - end of helix removed outlier: 3.824A pdb=" N THR B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 327 Processing helix chain 'B' and resid 335 through 364 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 376 through 404 removed outlier: 4.212A pdb=" N GLY B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 436 removed outlier: 3.589A pdb=" N LEU B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 529 through 558 Proline residue: B 541 - end of helix 500 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1136 1.33 - 1.45: 1756 1.45 - 1.57: 3800 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 6764 Sorted by residual: bond pdb=" CAX Y01 A 601 " pdb=" OAH Y01 A 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C GLN A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.52e+00 bond pdb=" C GLN B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.12e-02 7.97e+03 6.52e+00 bond pdb=" C ASN A 280 " pdb=" N VAL A 281 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.16e-02 7.43e+03 6.31e+00 ... (remaining 6759 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.77: 184 106.77 - 113.63: 3852 113.63 - 120.50: 2826 120.50 - 127.36: 2276 127.36 - 134.22: 72 Bond angle restraints: 9210 Sorted by residual: angle pdb=" CA GLY B 528 " pdb=" C GLY B 528 " pdb=" O GLY B 528 " ideal model delta sigma weight residual 122.22 119.74 2.48 6.50e-01 2.37e+00 1.46e+01 angle pdb=" CA GLY A 528 " pdb=" C GLY A 528 " pdb=" O GLY A 528 " ideal model delta sigma weight residual 122.22 119.74 2.48 6.50e-01 2.37e+00 1.46e+01 angle pdb=" C MET B 277 " pdb=" N TRP B 278 " pdb=" CA TRP B 278 " ideal model delta sigma weight residual 122.11 116.69 5.42 1.64e+00 3.72e-01 1.09e+01 angle pdb=" C MET A 277 " pdb=" N TRP A 278 " pdb=" CA TRP A 278 " ideal model delta sigma weight residual 122.11 116.69 5.42 1.64e+00 3.72e-01 1.09e+01 angle pdb=" CA TRP A 101 " pdb=" CB TRP A 101 " pdb=" CG TRP A 101 " ideal model delta sigma weight residual 113.60 107.43 6.17 1.90e+00 2.77e-01 1.06e+01 ... (remaining 9205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3344 16.85 - 33.70: 426 33.70 - 50.55: 84 50.55 - 67.39: 18 67.39 - 84.24: 10 Dihedral angle restraints: 3882 sinusoidal: 1484 harmonic: 2398 Sorted by residual: dihedral pdb=" CA ALA B 331 " pdb=" C ALA B 331 " pdb=" N PRO B 332 " pdb=" CA PRO B 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA A 331 " pdb=" C ALA A 331 " pdb=" N PRO A 332 " pdb=" CA PRO A 332 " ideal model delta harmonic sigma weight residual -180.00 -150.60 -29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN B 280 " pdb=" C ASN B 280 " pdb=" N VAL B 281 " pdb=" CA VAL B 281 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1002 0.093 - 0.185: 98 0.185 - 0.278: 6 0.278 - 0.370: 2 0.370 - 0.463: 2 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.79 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.57 -0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1107 not shown) Planarity restraints: 1082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 305 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 306 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 306 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 306 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 305 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 306 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 306 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 306 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 260 " 0.039 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO B 261 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.033 5.00e-02 4.00e+02 ... (remaining 1079 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2049 2.83 - 3.35: 6418 3.35 - 3.86: 11354 3.86 - 4.38: 12447 4.38 - 4.90: 22266 Nonbonded interactions: 54534 Sorted by model distance: nonbonded pdb=" O VAL B 338 " pdb=" OG SER B 342 " model vdw 2.309 2.440 nonbonded pdb=" O VAL A 338 " pdb=" OG SER A 342 " model vdw 2.309 2.440 nonbonded pdb=" O VAL B 65 " pdb=" OG SER B 69 " model vdw 2.315 2.440 nonbonded pdb=" O VAL A 65 " pdb=" OG SER A 69 " model vdw 2.315 2.440 nonbonded pdb=" O GLN A 190 " pdb=" OG1 THR A 194 " model vdw 2.328 2.440 ... (remaining 54529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 48 5.16 5 C 4428 2.51 5 N 1024 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.360 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.070 Process input model: 22.660 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 0.094 6764 Z= 0.440 Angle : 0.976 9.934 9210 Z= 0.513 Chirality : 0.060 0.463 1110 Planarity : 0.008 0.067 1082 Dihedral : 15.653 84.243 2334 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.51 % Favored : 95.24 % 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: -2.74 (0.24), residues: 798 helix: -1.19 (0.15), residues: 660 sheet: None (None), residues: 0 loop : -4.17 (0.48), residues: 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1599 time to fit residues: 44.4828 Evaluate side-chains 154 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 0.0070 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS A 520 ASN A 523 GLN B 515 HIS B 520 ASN B 523 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6764 Z= 0.164 Angle : 0.544 6.229 9210 Z= 0.286 Chirality : 0.039 0.134 1110 Planarity : 0.005 0.057 1082 Dihedral : 5.961 46.410 894 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 798 helix: 1.06 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -4.20 (0.52), residues: 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 191 average time/residue: 0.1607 time to fit residues: 42.0724 Evaluate side-chains 176 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0790 time to fit residues: 2.1003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN A 523 GLN B 520 ASN B 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6764 Z= 0.159 Angle : 0.532 6.515 9210 Z= 0.277 Chirality : 0.039 0.134 1110 Planarity : 0.004 0.053 1082 Dihedral : 5.636 48.069 894 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.30), residues: 798 helix: 1.87 (0.19), residues: 676 sheet: None (None), residues: 0 loop : -4.60 (0.48), residues: 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 182 average time/residue: 0.1572 time to fit residues: 39.2130 Evaluate side-chains 156 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0728 time to fit residues: 2.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 6764 Z= 0.165 Angle : 0.531 6.333 9210 Z= 0.275 Chirality : 0.039 0.186 1110 Planarity : 0.004 0.051 1082 Dihedral : 5.466 49.734 894 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.31), residues: 798 helix: 2.20 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -4.58 (0.50), residues: 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 171 average time/residue: 0.1549 time to fit residues: 36.4161 Evaluate side-chains 163 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0769 time to fit residues: 2.1030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 0.0070 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6764 Z= 0.154 Angle : 0.526 6.179 9210 Z= 0.276 Chirality : 0.040 0.181 1110 Planarity : 0.004 0.049 1082 Dihedral : 5.374 51.052 894 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.31), residues: 798 helix: 2.41 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -4.50 (0.51), residues: 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 173 average time/residue: 0.1766 time to fit residues: 40.7337 Evaluate side-chains 164 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0667 time to fit residues: 1.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6764 Z= 0.179 Angle : 0.542 6.876 9210 Z= 0.281 Chirality : 0.039 0.155 1110 Planarity : 0.004 0.049 1082 Dihedral : 5.370 53.254 894 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 2.49 % 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: 2.40 (0.31), residues: 798 helix: 2.52 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -4.41 (0.51), residues: 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.765 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 17 residues processed: 172 average time/residue: 0.1550 time to fit residues: 36.8755 Evaluate side-chains 175 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0775 time to fit residues: 3.3294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6764 Z= 0.226 Angle : 0.570 6.571 9210 Z= 0.296 Chirality : 0.042 0.175 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.519 56.458 894 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.31), residues: 798 helix: 2.54 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.20 (0.52), residues: 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 162 average time/residue: 0.1672 time to fit residues: 36.7516 Evaluate side-chains 158 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2457 time to fit residues: 1.9569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 6764 Z= 0.217 Angle : 0.575 7.427 9210 Z= 0.298 Chirality : 0.041 0.169 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.523 57.921 894 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 1.38 % 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: 2.31 (0.31), residues: 798 helix: 2.48 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.18 (0.51), residues: 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 165 average time/residue: 0.1630 time to fit residues: 36.9928 Evaluate side-chains 163 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 0.770 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0784 time to fit residues: 2.0044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 6764 Z= 0.174 Angle : 0.561 6.962 9210 Z= 0.292 Chirality : 0.041 0.243 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.386 57.556 894 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: 2.42 (0.31), residues: 798 helix: 2.55 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.11 (0.51), residues: 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 166 average time/residue: 0.1540 time to fit residues: 35.3173 Evaluate side-chains 159 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0618 time to fit residues: 1.2361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 6764 Z= 0.176 Angle : 0.567 7.060 9210 Z= 0.297 Chirality : 0.041 0.236 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.337 57.655 894 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.69 % 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: 2.44 (0.31), residues: 798 helix: 2.55 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.05 (0.51), residues: 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 158 average time/residue: 0.1599 time to fit residues: 34.8801 Evaluate side-chains 160 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0965 time to fit residues: 1.8865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN A 429 GLN B 429 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131112 restraints weight = 7979.732| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.71 r_work: 0.3373 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 6764 Z= 0.192 Angle : 0.566 7.138 9210 Z= 0.298 Chirality : 0.041 0.215 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.369 58.103 894 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.14 % 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: 2.48 (0.31), residues: 798 helix: 2.57 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -4.02 (0.51), residues: 126 =============================================================================== Job complete usr+sys time: 1669.36 seconds wall clock time: 30 minutes 57.21 seconds (1857.21 seconds total)