Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 11:51:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvh_34127/08_2023/7yvh_34127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvh_34127/08_2023/7yvh_34127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvh_34127/08_2023/7yvh_34127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvh_34127/08_2023/7yvh_34127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvh_34127/08_2023/7yvh_34127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvh_34127/08_2023/7yvh_34127.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 16 5.16 5 C 1988 2.51 5 N 530 2.21 5 O 590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 3124 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1441 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 2.08, per 1000 atoms: 0.67 Number of scatterers: 3124 At special positions: 0 Unit cell: (60.68, 70.52, 100.86, 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 16 16.00 O 590 8.00 N 530 7.00 C 1988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 524.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 6 sheets defined 9.5% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.074A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.152A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.910A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.817A pdb=" N GLU A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.579A pdb=" N LEU A 11 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 84 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.708A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.827A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.589A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 97 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 500 1.30 - 1.43: 919 1.43 - 1.56: 1763 1.56 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3202 Sorted by residual: bond pdb=" CA ARG C 97 " pdb=" C ARG C 97 " ideal model delta sigma weight residual 1.523 1.430 0.094 1.21e-02 6.83e+03 5.98e+01 bond pdb=" C ARG C 97 " pdb=" O ARG C 97 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.14e-02 7.69e+03 3.35e+01 bond pdb=" CB TYR B 473 " pdb=" CG TYR B 473 " ideal model delta sigma weight residual 1.512 1.421 0.091 2.20e-02 2.07e+03 1.70e+01 bond pdb=" CB TYR A 98 " pdb=" CG TYR A 98 " ideal model delta sigma weight residual 1.512 1.425 0.087 2.20e-02 2.07e+03 1.56e+01 bond pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 1.533 1.473 0.060 1.72e-02 3.38e+03 1.22e+01 ... (remaining 3197 not shown) Histogram of bond angle deviations from ideal: 92.80 - 101.09: 6 101.09 - 109.38: 330 109.38 - 117.67: 1967 117.67 - 125.96: 2012 125.96 - 134.25: 50 Bond angle restraints: 4365 Sorted by residual: angle pdb=" N GLN B 474 " pdb=" CA GLN B 474 " pdb=" C GLN B 474 " ideal model delta sigma weight residual 108.86 125.29 -16.43 1.41e+00 5.03e-01 1.36e+02 angle pdb=" C TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 110.43 92.80 17.63 1.68e+00 3.54e-01 1.10e+02 angle pdb=" O ILE B 472 " pdb=" C ILE B 472 " pdb=" N TYR B 473 " ideal model delta sigma weight residual 122.99 117.70 5.29 1.07e+00 8.73e-01 2.45e+01 angle pdb=" O TYR A 98 " pdb=" C TYR A 98 " pdb=" N THR A 99 " ideal model delta sigma weight residual 123.46 118.79 4.67 9.90e-01 1.02e+00 2.23e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 124.75 -10.35 2.30e+00 1.89e-01 2.03e+01 ... (remaining 4360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.23: 1763 23.23 - 46.46: 93 46.46 - 69.69: 13 69.69 - 92.92: 1 92.92 - 116.15: 1 Dihedral angle restraints: 1871 sinusoidal: 667 harmonic: 1204 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual -180.00 -63.85 -116.15 0 5.00e+00 4.00e-02 5.40e+02 dihedral pdb=" C TYR A 98 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta harmonic sigma weight residual -122.60 -101.20 -21.40 0 2.50e+00 1.60e-01 7.33e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 48.05 44.95 1 1.00e+01 1.00e-02 2.81e+01 ... (remaining 1868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 432 0.094 - 0.187: 40 0.187 - 0.280: 6 0.280 - 0.374: 1 0.374 - 0.467: 1 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA GLN B 474 " pdb=" N GLN B 474 " pdb=" C GLN B 474 " pdb=" CB GLN B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB THR C 112 " pdb=" CA THR C 112 " pdb=" OG1 THR C 112 " pdb=" CG2 THR C 112 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 477 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " -0.035 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" CG TRP A 94 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " 0.062 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 95 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 98 " 0.006 2.00e-02 2.50e+03 1.83e-02 6.68e+00 pdb=" CG TYR A 98 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 98 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 98 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 98 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 98 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 98 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 98 " -0.012 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 22 2.53 - 3.12: 2487 3.12 - 3.72: 4482 3.72 - 4.31: 6260 4.31 - 4.90: 10416 Nonbonded interactions: 23667 Sorted by model distance: nonbonded pdb=" CD ARG B 403 " pdb=" OD1 ASN B 405 " model vdw 1.941 3.440 nonbonded pdb=" O ARG C 31 " pdb=" OH TYR B 473 " model vdw 2.117 2.440 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR B 415 " model vdw 2.271 2.440 nonbonded pdb=" NZ LYS B 378 " pdb=" O CYS B 379 " model vdw 2.291 2.520 nonbonded pdb=" O TRP A 94 " pdb=" N GLY A 97 " model vdw 2.322 2.520 ... (remaining 23662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 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: 27.020 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.006 0.094 3202 Z= 0.437 Angle : 1.109 17.632 4365 Z= 0.649 Chirality : 0.063 0.467 480 Planarity : 0.006 0.092 566 Dihedral : 13.300 116.151 1091 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.70 % Favored : 90.82 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.34), residues: 414 helix: -4.90 (0.26), residues: 21 sheet: -1.77 (0.40), residues: 128 loop : -3.30 (0.31), residues: 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.1976 time to fit residues: 26.0243 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0285 time to fit residues: 0.6113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 3202 Z= 0.232 Angle : 0.788 19.533 4365 Z= 0.399 Chirality : 0.049 0.332 480 Planarity : 0.006 0.089 566 Dihedral : 5.161 50.518 459 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.11 % Favored : 95.41 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -2.68 (0.37), residues: 414 helix: -3.65 (0.66), residues: 23 sheet: -0.74 (0.44), residues: 123 loop : -2.24 (0.35), residues: 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.424 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1613 time to fit residues: 15.5349 Evaluate side-chains 63 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0377 time to fit residues: 1.1101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 12 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 3202 Z= 0.195 Angle : 0.680 15.710 4365 Z= 0.349 Chirality : 0.045 0.230 480 Planarity : 0.005 0.068 566 Dihedral : 5.006 46.476 459 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.25 % 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: -2.05 (0.39), residues: 414 helix: -2.78 (0.87), residues: 23 sheet: -0.53 (0.44), residues: 132 loop : -1.74 (0.37), residues: 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.350 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 73 average time/residue: 0.1454 time to fit residues: 13.0201 Evaluate side-chains 57 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0408 time to fit residues: 0.5407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 3202 Z= 0.272 Angle : 0.682 11.607 4365 Z= 0.354 Chirality : 0.045 0.156 480 Planarity : 0.005 0.074 566 Dihedral : 5.334 54.307 459 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.86 (0.41), residues: 414 helix: -2.68 (0.87), residues: 23 sheet: -0.49 (0.43), residues: 142 loop : -1.57 (0.40), residues: 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.360 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.1654 time to fit residues: 13.5628 Evaluate side-chains 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0406 time to fit residues: 1.1330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 3202 Z= 0.262 Angle : 0.693 9.986 4365 Z= 0.354 Chirality : 0.046 0.211 480 Planarity : 0.005 0.074 566 Dihedral : 5.320 55.891 459 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.81 (0.40), residues: 414 helix: -2.82 (0.82), residues: 23 sheet: -0.37 (0.43), residues: 137 loop : -1.57 (0.39), residues: 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.333 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.1651 time to fit residues: 12.9012 Evaluate side-chains 60 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0527 time to fit residues: 0.8453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 3202 Z= 0.196 Angle : 0.684 13.636 4365 Z= 0.346 Chirality : 0.046 0.170 480 Planarity : 0.005 0.070 566 Dihedral : 4.981 50.444 459 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.63 (0.40), residues: 414 helix: -2.63 (0.86), residues: 23 sheet: -0.06 (0.46), residues: 123 loop : -1.50 (0.37), residues: 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.347 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.1690 time to fit residues: 13.6504 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0427 time to fit residues: 0.7736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.0370 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 3202 Z= 0.200 Angle : 0.683 12.025 4365 Z= 0.348 Chirality : 0.046 0.219 480 Planarity : 0.005 0.065 566 Dihedral : 4.804 47.738 459 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.48 (0.40), residues: 414 helix: -2.51 (0.89), residues: 23 sheet: -0.07 (0.45), residues: 129 loop : -1.37 (0.38), residues: 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.360 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 65 average time/residue: 0.1727 time to fit residues: 13.5315 Evaluate side-chains 60 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0481 time to fit residues: 0.6265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.0010 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 3202 Z= 0.193 Angle : 0.683 12.513 4365 Z= 0.345 Chirality : 0.045 0.181 480 Planarity : 0.005 0.064 566 Dihedral : 4.723 46.025 459 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.41 (0.40), residues: 414 helix: -2.38 (0.91), residues: 23 sheet: 0.07 (0.46), residues: 126 loop : -1.36 (0.38), residues: 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.333 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.1673 time to fit residues: 12.6184 Evaluate side-chains 61 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0319 time to fit residues: 0.6175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 chunk 36 optimal weight: 0.0040 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 3202 Z= 0.180 Angle : 0.716 12.202 4365 Z= 0.358 Chirality : 0.045 0.202 480 Planarity : 0.005 0.064 566 Dihedral : 4.622 44.239 459 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.36 (0.40), residues: 414 helix: -2.30 (0.92), residues: 23 sheet: 0.11 (0.46), residues: 129 loop : -1.35 (0.37), residues: 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.354 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 0.2029 time to fit residues: 14.9448 Evaluate side-chains 59 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0334 time to fit residues: 0.5267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 3202 Z= 0.191 Angle : 0.709 12.066 4365 Z= 0.350 Chirality : 0.045 0.166 480 Planarity : 0.005 0.062 566 Dihedral : 4.669 44.140 459 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.23 (0.40), residues: 414 helix: -2.65 (0.88), residues: 22 sheet: 0.22 (0.46), residues: 128 loop : -1.22 (0.38), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.366 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1860 time to fit residues: 12.8685 Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0358 time to fit residues: 0.5978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.0270 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.118035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.097789 restraints weight = 8186.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100403 restraints weight = 4466.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102170 restraints weight = 3039.086| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 3202 Z= 0.184 Angle : 0.703 11.992 4365 Z= 0.350 Chirality : 0.044 0.206 480 Planarity : 0.005 0.062 566 Dihedral : 4.513 43.839 459 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.09 (0.41), residues: 414 helix: -1.93 (1.01), residues: 23 sheet: 0.38 (0.47), residues: 125 loop : -1.21 (0.37), residues: 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1435.81 seconds wall clock time: 26 minutes 15.85 seconds (1575.85 seconds total)