Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 09:18:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/04_2023/6nf6_9361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/04_2023/6nf6_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_9361/04_2023/6nf6_9361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/04_2023/6nf6_9361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/04_2023/6nf6_9361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf6_9361/04_2023/6nf6_9361.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 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. 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-1.21rc1-4938/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: 4.16, per 1000 atoms: 0.63 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: 2.64 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... Secondary structure from input PDB file: 28 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 49 through 78 removed outlier: 3.964A pdb=" N GLY A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'A' and resid 127 through 152 Processing helix chain 'A' and resid 162 through 182 removed outlier: 3.724A pdb=" N HIS A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 215 Processing helix chain 'A' and resid 216 through 226 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 248 through 280 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 328 Processing helix chain 'A' and resid 334 through 365 removed outlier: 3.812A pdb=" N VAL A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 376 through 405 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) removed outlier: 3.674A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 437 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 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 528 through 559 Proline residue: A 541 - end of helix removed outlier: 3.525A pdb=" N VAL A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 78 Processing helix chain 'B' and resid 83 through 109 Processing helix chain 'B' and resid 127 through 152 Processing helix chain 'B' and resid 162 through 182 removed outlier: 3.724A pdb=" N HIS B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 215 Processing helix chain 'B' and resid 216 through 226 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 248 through 280 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 328 Processing helix chain 'B' and resid 334 through 365 removed outlier: 3.812A pdb=" N VAL B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 376 through 405 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) removed outlier: 3.674A pdb=" N THR B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 437 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 509 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 528 through 559 Proline residue: B 541 - end of helix removed outlier: 3.525A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1608 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: 1.84 Time building geometry restraints manager: 2.86 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: 6386 3.35 - 3.86: 11322 3.86 - 4.38: 12375 4.38 - 4.90: 22258 Nonbonded interactions: 54390 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 54385 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 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: 0.330 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: 2.360 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 21.690 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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= 0.445 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 : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1668 time to fit residues: 46.3122 Evaluate side-chains 154 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0757 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6764 Z= 0.167 Angle : 0.561 6.008 9210 Z= 0.297 Chirality : 0.039 0.134 1110 Planarity : 0.005 0.057 1082 Dihedral : 6.114 45.950 894 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: 0.41 (0.29), residues: 798 helix: 1.07 (0.18), residues: 674 sheet: None (None), residues: 0 loop : -4.15 (0.52), residues: 124 *********************** 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 211 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 203 average time/residue: 0.1642 time to fit residues: 45.2933 Evaluate side-chains 187 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0789 time to fit residues: 2.1043 ------------------------------------------------------------------------------- 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: 3.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6764 Z= 0.224 Angle : 0.572 6.689 9210 Z= 0.299 Chirality : 0.041 0.203 1110 Planarity : 0.004 0.053 1082 Dihedral : 5.913 48.444 894 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 3.18 % 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: 1.26 (0.30), residues: 798 helix: 1.71 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.75 (0.51), residues: 116 *********************** 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 211 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 198 average time/residue: 0.1644 time to fit residues: 44.4116 Evaluate side-chains 178 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0668 time to fit residues: 2.3879 ------------------------------------------------------------------------------- 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: 3.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2157 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= 0.182 Angle : 0.552 6.272 9210 Z= 0.290 Chirality : 0.040 0.200 1110 Planarity : 0.004 0.051 1082 Dihedral : 5.673 49.798 894 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.52 % 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: 1.80 (0.31), residues: 798 helix: 2.08 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.76 (0.52), residues: 114 *********************** 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 195 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 186 average time/residue: 0.1503 time to fit residues: 38.7657 Evaluate side-chains 178 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0772 time to fit residues: 2.2270 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 6764 Z= 0.196 Angle : 0.558 6.217 9210 Z= 0.294 Chirality : 0.041 0.173 1110 Planarity : 0.004 0.050 1082 Dihedral : 5.601 52.226 894 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.97 % 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: 1.97 (0.31), residues: 798 helix: 2.21 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -4.75 (0.52), residues: 114 *********************** 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 184 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 181 average time/residue: 0.1582 time to fit residues: 39.7092 Evaluate side-chains 166 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0639 time to fit residues: 1.6705 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6764 Z= 0.187 Angle : 0.557 7.370 9210 Z= 0.294 Chirality : 0.040 0.201 1110 Planarity : 0.004 0.049 1082 Dihedral : 5.517 53.814 894 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.76 % 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: 2.12 (0.31), residues: 798 helix: 2.34 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.75 (0.51), residues: 116 *********************** 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 195 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 184 average time/residue: 0.1691 time to fit residues: 42.0194 Evaluate side-chains 179 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0746 time to fit residues: 3.0899 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 6764 Z= 0.243 Angle : 0.590 7.216 9210 Z= 0.308 Chirality : 0.041 0.166 1110 Planarity : 0.004 0.049 1082 Dihedral : 5.627 56.869 894 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 1.52 % 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: 2.11 (0.31), residues: 798 helix: 2.30 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.53 (0.56), residues: 116 *********************** 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 185 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 181 average time/residue: 0.1607 time to fit residues: 40.0735 Evaluate side-chains 168 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 163 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0647 time to fit residues: 1.6575 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 6764 Z= 0.217 Angle : 0.587 6.928 9210 Z= 0.311 Chirality : 0.041 0.199 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.592 57.196 894 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: 2.18 (0.31), residues: 798 helix: 2.34 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.52 (0.53), residues: 116 *********************** 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 181 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 173 average time/residue: 0.1633 time to fit residues: 38.8366 Evaluate side-chains 167 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0832 time to fit residues: 2.4362 ------------------------------------------------------------------------------- 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: 0.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 77 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7805 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 6764 Z= 0.206 Angle : 0.594 6.766 9210 Z= 0.314 Chirality : 0.040 0.169 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.500 57.232 894 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.97 % 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: 2.25 (0.31), residues: 798 helix: 2.39 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.48 (0.53), residues: 116 *********************** 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 172 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 171 average time/residue: 0.1447 time to fit residues: 34.4921 Evaluate side-chains 160 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0620 time to fit residues: 1.2917 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 6764 Z= 0.239 Angle : 0.616 7.049 9210 Z= 0.327 Chirality : 0.043 0.207 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.634 58.104 894 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.97 % 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: 2.18 (0.31), residues: 798 helix: 2.35 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.43 (0.54), residues: 118 ********************** 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 166 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 162 average time/residue: 0.1620 time to fit residues: 36.3790 Evaluate side-chains 158 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0762 time to fit residues: 1.6755 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.157386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131711 restraints weight = 7936.507| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.72 r_work: 0.3388 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 6764 Z= 0.204 Angle : 0.601 6.973 9210 Z= 0.318 Chirality : 0.042 0.189 1110 Planarity : 0.004 0.048 1082 Dihedral : 5.485 56.853 894 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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: 2.24 (0.31), residues: 798 helix: 2.37 (0.19), residues: 682 sheet: None (None), residues: 0 loop : -4.40 (0.53), residues: 116 =============================================================================== Job complete usr+sys time: 1604.39 seconds wall clock time: 29 minutes 46.02 seconds (1786.02 seconds total)