Sun 23 Dec 22:22:43 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2otm-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2otm-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:53 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2otm-3.4-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 388 and 0 Target number of residues in the AU: 388 Target solvent content: 0.6205 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 462 Adjusted target solvent content: 0.55 Input MTZ file: 2otm-3.4-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 5 Cell parameters: 112.035 62.893 78.663 90.000 93.262 90.000 Input sequence file: 2otm-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3696 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 78.536 3.400 Wilson plot Bfac: 61.75 7660 reflections ( 99.80 % complete ) and 0 restraints for refining 4094 atoms. Observations/parameters ratio is 0.47 ------------------------------------------------------ Starting model: R = 0.2991 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2628 (Rfree = 0.000) for 4094 atoms. Found 30 (30 requested) and removed 32 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 4159 seeds are put forward NCS extension: 0 residues added, 4159 seeds are put forward Round 1: 250 peptides, 41 chains. Longest chain 11 peptides. Score 0.439 Round 2: 312 peptides, 36 chains. Longest chain 19 peptides. Score 0.639 Round 3: 312 peptides, 34 chains. Longest chain 28 peptides. Score 0.657 Round 4: 320 peptides, 33 chains. Longest chain 30 peptides. Score 0.680 Round 5: 339 peptides, 36 chains. Longest chain 28 peptides. Score 0.689 Taking the results from Round 5 Chains 41, Residues 303, Estimated correctness of the model 55.0 % 9 chains (105 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6092 restraints for refining 3359 atoms. 4550 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2546 (Rfree = 0.000) for 3359 atoms. Found 20 (25 requested) and removed 41 (12 requested) atoms. Cycle 2: After refmac, R = 0.2411 (Rfree = 0.000) for 3294 atoms. Found 14 (25 requested) and removed 28 (12 requested) atoms. Cycle 3: After refmac, R = 0.2373 (Rfree = 0.000) for 3262 atoms. Found 8 (24 requested) and removed 18 (12 requested) atoms. Cycle 4: After refmac, R = 0.2336 (Rfree = 0.000) for 3239 atoms. Found 8 (24 requested) and removed 20 (12 requested) atoms. Cycle 5: After refmac, R = 0.2335 (Rfree = 0.000) for 3221 atoms. Found 7 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 3310 seeds are put forward NCS extension: 11 residues added (13 deleted due to clashes), 3321 seeds are put forward Round 1: 291 peptides, 38 chains. Longest chain 27 peptides. Score 0.575 Round 2: 324 peptides, 35 chains. Longest chain 31 peptides. Score 0.670 Round 3: 321 peptides, 37 chains. Longest chain 23 peptides. Score 0.647 Round 4: 317 peptides, 34 chains. Longest chain 27 peptides. Score 0.666 Round 5: 318 peptides, 34 chains. Longest chain 22 peptides. Score 0.668 Taking the results from Round 2 Chains 37, Residues 289, Estimated correctness of the model 49.8 % 4 chains (72 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6627 restraints for refining 3360 atoms. 5231 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2480 (Rfree = 0.000) for 3360 atoms. Found 17 (25 requested) and removed 34 (12 requested) atoms. Cycle 7: After refmac, R = 0.2348 (Rfree = 0.000) for 3330 atoms. Found 5 (25 requested) and removed 20 (12 requested) atoms. Cycle 8: After refmac, R = 0.2226 (Rfree = 0.000) for 3311 atoms. Found 0 (25 requested) and removed 15 (12 requested) atoms. Cycle 9: After refmac, R = 0.2170 (Rfree = 0.000) for 3293 atoms. Found 4 (24 requested) and removed 15 (12 requested) atoms. Cycle 10: After refmac, R = 0.2096 (Rfree = 0.000) for 3278 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 3362 seeds are put forward NCS extension: 10 residues added (18 deleted due to clashes), 3372 seeds are put forward Round 1: 290 peptides, 40 chains. Longest chain 18 peptides. Score 0.552 Round 2: 327 peptides, 38 chains. Longest chain 22 peptides. Score 0.650 Round 3: 317 peptides, 38 chains. Longest chain 22 peptides. Score 0.630 Round 4: 325 peptides, 36 chains. Longest chain 22 peptides. Score 0.664 Round 5: 325 peptides, 37 chains. Longest chain 22 peptides. Score 0.655 Taking the results from Round 4 Chains 36, Residues 289, Estimated correctness of the model 48.2 % 4 chains (48 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6833 restraints for refining 3360 atoms. 5542 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2209 (Rfree = 0.000) for 3360 atoms. Found 23 (25 requested) and removed 22 (12 requested) atoms. Cycle 12: After refmac, R = 0.1988 (Rfree = 0.000) for 3353 atoms. Found 6 (25 requested) and removed 16 (12 requested) atoms. Cycle 13: After refmac, R = 0.1952 (Rfree = 0.000) for 3338 atoms. Found 3 (25 requested) and removed 17 (12 requested) atoms. Cycle 14: After refmac, R = 0.1904 (Rfree = 0.000) for 3320 atoms. Found 3 (25 requested) and removed 14 (12 requested) atoms. Cycle 15: After refmac, R = 0.1799 (Rfree = 0.000) for 3308 atoms. Found 3 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.20 2.99 Search for helices and strands: 0 residues in 0 chains, 3369 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 3385 seeds are put forward Round 1: 302 peptides, 41 chains. Longest chain 18 peptides. Score 0.569 Round 2: 321 peptides, 37 chains. Longest chain 23 peptides. Score 0.647 Round 3: 323 peptides, 35 chains. Longest chain 29 peptides. Score 0.668 Round 4: 323 peptides, 37 chains. Longest chain 25 peptides. Score 0.651 Round 5: 330 peptides, 33 chains. Longest chain 36 peptides. Score 0.698 Taking the results from Round 5 Chains 37, Residues 297, Estimated correctness of the model 57.4 % 3 chains (49 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6530 restraints for refining 3361 atoms. 5193 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2339 (Rfree = 0.000) for 3361 atoms. Found 21 (25 requested) and removed 33 (12 requested) atoms. Cycle 17: After refmac, R = 0.2107 (Rfree = 0.000) for 3320 atoms. Found 11 (25 requested) and removed 15 (12 requested) atoms. Cycle 18: After refmac, R = 0.2048 (Rfree = 0.000) for 3304 atoms. Found 7 (25 requested) and removed 15 (12 requested) atoms. Cycle 19: After refmac, R = 0.1995 (Rfree = 0.000) for 3288 atoms. Found 4 (24 requested) and removed 14 (12 requested) atoms. Cycle 20: After refmac, R = 0.1937 (Rfree = 0.000) for 3275 atoms. Found 3 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.21 3.00 Search for helices and strands: 0 residues in 0 chains, 3359 seeds are put forward NCS extension: 15 residues added (14 deleted due to clashes), 3374 seeds are put forward Round 1: 287 peptides, 41 chains. Longest chain 17 peptides. Score 0.534 Round 2: 299 peptides, 36 chains. Longest chain 21 peptides. Score 0.612 Round 3: 314 peptides, 32 chains. Longest chain 23 peptides. Score 0.678 Round 4: 327 peptides, 39 chains. Longest chain 28 peptides. Score 0.641 Round 5: 319 peptides, 37 chains. Longest chain 29 peptides. Score 0.643 Taking the results from Round 3 Chains 33, Residues 282, Estimated correctness of the model 52.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7077 restraints for refining 3360 atoms. 5923 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2155 (Rfree = 0.000) for 3360 atoms. Found 9 (25 requested) and removed 33 (12 requested) atoms. Cycle 22: After refmac, R = 0.1996 (Rfree = 0.000) for 3327 atoms. Found 4 (25 requested) and removed 17 (12 requested) atoms. Cycle 23: After refmac, R = 0.1964 (Rfree = 0.000) for 3308 atoms. Found 5 (25 requested) and removed 17 (12 requested) atoms. Cycle 24: After refmac, R = 0.1943 (Rfree = 0.000) for 3292 atoms. Found 6 (24 requested) and removed 14 (12 requested) atoms. Cycle 25: After refmac, R = 0.1879 (Rfree = 0.000) for 3283 atoms. Found 4 (24 requested) and removed 15 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.19 2.98 Search for helices and strands: 0 residues in 0 chains, 3347 seeds are put forward NCS extension: 23 residues added (5 deleted due to clashes), 3370 seeds are put forward Round 1: 299 peptides, 46 chains. Longest chain 18 peptides. Score 0.510 Round 2: 317 peptides, 36 chains. Longest chain 40 peptides. Score 0.648 Round 3: 308 peptides, 35 chains. Longest chain 26 peptides. Score 0.640 Round 4: 321 peptides, 39 chains. Longest chain 23 peptides. Score 0.629 Round 5: 304 peptides, 36 chains. Longest chain 30 peptides. Score 0.622 Taking the results from Round 2 Chains 38, Residues 281, Estimated correctness of the model 43.6 % 2 chains (35 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7060 restraints for refining 3361 atoms. 5844 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2108 (Rfree = 0.000) for 3361 atoms. Found 10 (25 requested) and removed 21 (12 requested) atoms. Cycle 27: After refmac, R = 0.1978 (Rfree = 0.000) for 3346 atoms. Found 2 (25 requested) and removed 12 (12 requested) atoms. Cycle 28: After refmac, R = 0.1968 (Rfree = 0.000) for 3331 atoms. Found 1 (25 requested) and removed 12 (12 requested) atoms. Cycle 29: After refmac, R = 0.1892 (Rfree = 0.000) for 3316 atoms. Found 0 (25 requested) and removed 13 (12 requested) atoms. Cycle 30: After refmac, R = 0.1849 (Rfree = 0.000) for 3303 atoms. Found 2 (24 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.20 2.99 Search for helices and strands: 0 residues in 0 chains, 3365 seeds are put forward NCS extension: 22 residues added (15 deleted due to clashes), 3387 seeds are put forward Round 1: 281 peptides, 42 chains. Longest chain 20 peptides. Score 0.509 Round 2: 296 peptides, 33 chains. Longest chain 33 peptides. Score 0.634 Round 3: 314 peptides, 39 chains. Longest chain 21 peptides. Score 0.615 Round 4: 295 peptides, 34 chains. Longest chain 33 peptides. Score 0.623 Round 5: 310 peptides, 34 chains. Longest chain 39 peptides. Score 0.653 Taking the results from Round 5 Chains 36, Residues 276, Estimated correctness of the model 45.0 % 2 chains (42 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6900 restraints for refining 3361 atoms. 5659 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2189 (Rfree = 0.000) for 3361 atoms. Found 11 (25 requested) and removed 21 (12 requested) atoms. Cycle 32: After refmac, R = 0.2038 (Rfree = 0.000) for 3345 atoms. Found 3 (25 requested) and removed 16 (12 requested) atoms. Cycle 33: After refmac, R = 0.1972 (Rfree = 0.000) for 3331 atoms. Found 5 (25 requested) and removed 15 (12 requested) atoms. Cycle 34: After refmac, R = 0.1909 (Rfree = 0.000) for 3318 atoms. Found 4 (25 requested) and removed 13 (12 requested) atoms. Cycle 35: After refmac, R = 0.1936 (Rfree = 0.000) for 3305 atoms. Found 4 (24 requested) and removed 13 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 3369 seeds are put forward NCS extension: 36 residues added (10 deleted due to clashes), 3405 seeds are put forward Round 1: 271 peptides, 39 chains. Longest chain 18 peptides. Score 0.517 Round 2: 285 peptides, 38 chains. Longest chain 16 peptides. Score 0.561 Round 3: 283 peptides, 37 chains. Longest chain 15 peptides. Score 0.567 Round 4: 302 peptides, 38 chains. Longest chain 18 peptides. Score 0.599 Round 5: 283 peptides, 34 chains. Longest chain 20 peptides. Score 0.597 Taking the results from Round 4 Chains 40, Residues 264, Estimated correctness of the model 28.3 % 5 chains (45 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 6881 restraints for refining 3361 atoms. 5714 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2313 (Rfree = 0.000) for 3361 atoms. Found 13 (25 requested) and removed 18 (12 requested) atoms. Cycle 37: After refmac, R = 0.2059 (Rfree = 0.000) for 3351 atoms. Found 5 (25 requested) and removed 13 (12 requested) atoms. Cycle 38: After refmac, R = 0.1984 (Rfree = 0.000) for 3337 atoms. Found 5 (25 requested) and removed 12 (12 requested) atoms. Cycle 39: After refmac, R = 0.1913 (Rfree = 0.000) for 3328 atoms. Found 4 (25 requested) and removed 12 (12 requested) atoms. Cycle 40: After refmac, R = 0.2078 (Rfree = 0.000) for 3316 atoms. Found 10 (25 requested) and removed 12 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 3402 seeds are put forward NCS extension: 17 residues added (2 deleted due to clashes), 3419 seeds are put forward Round 1: 237 peptides, 39 chains. Longest chain 17 peptides. Score 0.427 Round 2: 272 peptides, 40 chains. Longest chain 18 peptides. Score 0.508 Round 3: 271 peptides, 38 chains. Longest chain 20 peptides. Score 0.528 Round 4: 276 peptides, 37 chains. Longest chain 21 peptides. Score 0.550 Round 5: 271 peptides, 35 chains. Longest chain 16 peptides. Score 0.560 Taking the results from Round 5 Chains 37, Residues 236, Estimated correctness of the model 15.1 % 3 chains (30 residues) have been docked in sequence ------------------------------------------------------ 7660 reflections ( 99.80 % complete ) and 7271 restraints for refining 3361 atoms. 6259 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2143 (Rfree = 0.000) for 3361 atoms. Found 12 (25 requested) and removed 19 (12 requested) atoms. Cycle 42: After refmac, R = 0.2085 (Rfree = 0.000) for 3344 atoms. Found 6 (25 requested) and removed 15 (12 requested) atoms. Cycle 43: After refmac, R = 0.2096 (Rfree = 0.000) for 3327 atoms. Found 8 (25 requested) and removed 14 (12 requested) atoms. Cycle 44: After refmac, R = 0.2107 (Rfree = 0.000) for 3317 atoms. Found 13 (25 requested) and removed 13 (12 requested) atoms. Cycle 45: After refmac, R = 0.2599 (Rfree = 0.000) for 3308 atoms. Found 25 (25 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.97 Search for helices and strands: 0 residues in 0 chains, 3415 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3428 seeds are put forward Round 1: 206 peptides, 38 chains. Longest chain 13 peptides. Score 0.348 Round 2: 235 peptides, 36 chains. Longest chain 17 peptides. Score 0.457 Round 3: 240 peptides, 36 chains. Longest chain 19 peptides. Score 0.471 Round 4: 239 peptides, 35 chains. Longest chain 18 peptides. Score 0.480 Round 5: 255 peptides, 33 chains. Longest chain 25 peptides. Score 0.543 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 222, Estimated correctness of the model 9.0 % 3 chains (43 residues) have been docked in sequence Sequence coverage is 19 % Consider running further cycles of model building using 2otm-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (222 residues) following loop building 3 chains (43 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7660 reflections ( 99.80 % complete ) and 7163 restraints for refining 3361 atoms. 6143 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2146 (Rfree = 0.000) for 3361 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.2079 (Rfree = 0.000) for 3330 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1918 (Rfree = 0.000) for 3309 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1899 (Rfree = 0.000) for 3295 atoms. TimeTaking 56.93