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 1vk3-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vk3-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.4-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/1vk3-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.4-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/1vk3-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vk3-3.4-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 452 and 0 Target number of residues in the AU: 452 Target solvent content: 0.5621 Checking the provided sequence file Detected sequence length: 615 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 615 Adjusted target solvent content: 0.40 Input MTZ file: 1vk3-3.4-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: 19 Cell parameters: 59.785 72.683 128.550 90.000 90.000 90.000 Input sequence file: 1vk3-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4920 target number of atoms Had to go as low as 0.55 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 Loops will be built when appropriate and at the last cycle Resolution range: 30.186 3.400 Wilson plot Bfac: 38.95 8022 reflections ( 98.42 % complete ) and 0 restraints for refining 5472 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3121 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2663 (Rfree = 0.000) for 5472 atoms. Found 41 (41 requested) and removed 53 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.92 3.34 Search for helices and strands: 0 residues in 0 chains, 5564 seeds are put forward Round 1: 189 peptides, 41 chains. Longest chain 7 peptides. Score 0.253 Round 2: 249 peptides, 44 chains. Longest chain 12 peptides. Score 0.398 Round 3: 280 peptides, 47 chains. Longest chain 12 peptides. Score 0.448 Round 4: 287 peptides, 46 chains. Longest chain 16 peptides. Score 0.478 Round 5: 298 peptides, 42 chains. Longest chain 15 peptides. Score 0.547 Taking the results from Round 5 Chains 45, Residues 256, Estimated correctness of the model 10.4 % 9 chains (57 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9965 restraints for refining 4473 atoms. 8839 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2352 (Rfree = 0.000) for 4473 atoms. Found 33 (33 requested) and removed 42 (16 requested) atoms. Cycle 2: After refmac, R = 0.2170 (Rfree = 0.000) for 4401 atoms. Found 17 (33 requested) and removed 30 (16 requested) atoms. Cycle 3: After refmac, R = 0.2125 (Rfree = 0.000) for 4362 atoms. Found 14 (33 requested) and removed 23 (16 requested) atoms. Cycle 4: After refmac, R = 0.2020 (Rfree = 0.000) for 4334 atoms. Found 12 (32 requested) and removed 20 (16 requested) atoms. Cycle 5: After refmac, R = 0.1959 (Rfree = 0.000) for 4316 atoms. Found 13 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.93 3.35 Search for helices and strands: 0 residues in 0 chains, 4443 seeds are put forward Round 1: 249 peptides, 42 chains. Longest chain 15 peptides. Score 0.422 Round 2: 291 peptides, 45 chains. Longest chain 17 peptides. Score 0.499 Round 3: 318 peptides, 46 chains. Longest chain 16 peptides. Score 0.553 Round 4: 311 peptides, 45 chains. Longest chain 16 peptides. Score 0.547 Round 5: 312 peptides, 43 chains. Longest chain 16 peptides. Score 0.569 Taking the results from Round 5 Chains 44, Residues 269, Estimated correctness of the model 18.2 % 7 chains (44 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9709 restraints for refining 4324 atoms. 8568 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2240 (Rfree = 0.000) for 4324 atoms. Found 24 (32 requested) and removed 39 (16 requested) atoms. Cycle 7: After refmac, R = 0.2113 (Rfree = 0.000) for 4293 atoms. Found 20 (32 requested) and removed 28 (16 requested) atoms. Cycle 8: After refmac, R = 0.2062 (Rfree = 0.000) for 4277 atoms. Found 17 (32 requested) and removed 30 (16 requested) atoms. Cycle 9: After refmac, R = 0.1993 (Rfree = 0.000) for 4259 atoms. Found 12 (32 requested) and removed 30 (16 requested) atoms. Cycle 10: After refmac, R = 0.1984 (Rfree = 0.000) for 4238 atoms. Found 32 (32 requested) and removed 28 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.91 3.33 Search for helices and strands: 0 residues in 0 chains, 4393 seeds are put forward Round 1: 249 peptides, 47 chains. Longest chain 12 peptides. Score 0.361 Round 2: 304 peptides, 43 chains. Longest chain 21 peptides. Score 0.551 Round 3: 296 peptides, 42 chains. Longest chain 15 peptides. Score 0.543 Round 4: 312 peptides, 45 chains. Longest chain 16 peptides. Score 0.549 Round 5: 322 peptides, 41 chains. Longest chain 24 peptides. Score 0.610 Taking the results from Round 5 Chains 42, Residues 281, Estimated correctness of the model 31.9 % 3 chains (29 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9943 restraints for refining 4473 atoms. 8744 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2253 (Rfree = 0.000) for 4473 atoms. Found 24 (33 requested) and removed 35 (16 requested) atoms. Cycle 12: After refmac, R = 0.2060 (Rfree = 0.000) for 4446 atoms. Found 13 (33 requested) and removed 31 (16 requested) atoms. Cycle 13: After refmac, R = 0.1952 (Rfree = 0.000) for 4415 atoms. Found 13 (33 requested) and removed 27 (16 requested) atoms. Cycle 14: After refmac, R = 0.1898 (Rfree = 0.000) for 4394 atoms. Found 11 (33 requested) and removed 21 (16 requested) atoms. Cycle 15: After refmac, R = 0.1886 (Rfree = 0.000) for 4378 atoms. Found 13 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 3.31 Search for helices and strands: 0 residues in 0 chains, 4492 seeds are put forward Round 1: 258 peptides, 46 chains. Longest chain 13 peptides. Score 0.399 Round 2: 288 peptides, 43 chains. Longest chain 23 peptides. Score 0.513 Round 3: 307 peptides, 44 chains. Longest chain 22 peptides. Score 0.548 Round 4: 315 peptides, 46 chains. Longest chain 18 peptides. Score 0.546 Round 5: 316 peptides, 41 chains. Longest chain 22 peptides. Score 0.598 Taking the results from Round 5 Chains 45, Residues 275, Estimated correctness of the model 28.0 % 8 chains (59 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9657 restraints for refining 4473 atoms. 8424 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2234 (Rfree = 0.000) for 4473 atoms. Found 29 (33 requested) and removed 40 (16 requested) atoms. Cycle 17: After refmac, R = 0.2091 (Rfree = 0.000) for 4450 atoms. Found 21 (33 requested) and removed 23 (16 requested) atoms. Cycle 18: After refmac, R = 0.1987 (Rfree = 0.000) for 4430 atoms. Found 14 (33 requested) and removed 22 (16 requested) atoms. Cycle 19: After refmac, R = 0.1912 (Rfree = 0.000) for 4413 atoms. Found 10 (33 requested) and removed 20 (16 requested) atoms. Cycle 20: After refmac, R = 0.1888 (Rfree = 0.000) for 4399 atoms. Found 14 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 3.31 Search for helices and strands: 0 residues in 0 chains, 4538 seeds are put forward Round 1: 233 peptides, 40 chains. Longest chain 12 peptides. Score 0.401 Round 2: 246 peptides, 39 chains. Longest chain 13 peptides. Score 0.450 Round 3: 284 peptides, 44 chains. Longest chain 18 peptides. Score 0.492 Round 4: 281 peptides, 39 chains. Longest chain 20 peptides. Score 0.539 Round 5: 280 peptides, 43 chains. Longest chain 16 peptides. Score 0.493 Taking the results from Round 4 Chains 41, Residues 242, Estimated correctness of the model 7.5 % 8 chains (57 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9896 restraints for refining 4463 atoms. 8809 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2051 (Rfree = 0.000) for 4463 atoms. Found 21 (33 requested) and removed 57 (16 requested) atoms. Cycle 22: After refmac, R = 0.1912 (Rfree = 0.000) for 4411 atoms. Found 21 (33 requested) and removed 25 (16 requested) atoms. Cycle 23: After refmac, R = 0.1833 (Rfree = 0.000) for 4397 atoms. Found 9 (33 requested) and removed 21 (16 requested) atoms. Cycle 24: After refmac, R = 0.1755 (Rfree = 0.000) for 4377 atoms. Found 7 (33 requested) and removed 17 (16 requested) atoms. Cycle 25: After refmac, R = 0.1773 (Rfree = 0.000) for 4361 atoms. Found 3 (32 requested) and removed 16 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.89 3.31 Search for helices and strands: 0 residues in 0 chains, 4452 seeds are put forward Round 1: 252 peptides, 48 chains. Longest chain 12 peptides. Score 0.358 Round 2: 293 peptides, 47 chains. Longest chain 26 peptides. Score 0.482 Round 3: 305 peptides, 48 chains. Longest chain 15 peptides. Score 0.501 Round 4: 297 peptides, 45 chains. Longest chain 23 peptides. Score 0.514 Round 5: 312 peptides, 45 chains. Longest chain 19 peptides. Score 0.549 Taking the results from Round 5 Chains 47, Residues 267, Estimated correctness of the model 11.2 % 4 chains (27 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9991 restraints for refining 4473 atoms. 8902 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2072 (Rfree = 0.000) for 4473 atoms. Found 16 (33 requested) and removed 33 (16 requested) atoms. Cycle 27: After refmac, R = 0.2025 (Rfree = 0.000) for 4443 atoms. Found 15 (33 requested) and removed 25 (16 requested) atoms. Cycle 28: After refmac, R = 0.1939 (Rfree = 0.000) for 4419 atoms. Found 14 (33 requested) and removed 20 (16 requested) atoms. Cycle 29: After refmac, R = 0.1860 (Rfree = 0.000) for 4410 atoms. Found 14 (33 requested) and removed 23 (16 requested) atoms. Cycle 30: After refmac, R = 0.1767 (Rfree = 0.000) for 4397 atoms. Found 11 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.91 3.33 Search for helices and strands: 0 residues in 0 chains, 4506 seeds are put forward Round 1: 230 peptides, 44 chains. Longest chain 17 peptides. Score 0.342 Round 2: 273 peptides, 46 chains. Longest chain 19 peptides. Score 0.441 Round 3: 275 peptides, 46 chains. Longest chain 24 peptides. Score 0.446 Round 4: 307 peptides, 43 chains. Longest chain 26 peptides. Score 0.558 Round 5: 299 peptides, 48 chains. Longest chain 15 peptides. Score 0.486 Taking the results from Round 4 Chains 48, Residues 264, Estimated correctness of the model 14.4 % 7 chains (64 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 9535 restraints for refining 4473 atoms. 8291 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2088 (Rfree = 0.000) for 4473 atoms. Found 16 (33 requested) and removed 27 (16 requested) atoms. Cycle 32: After refmac, R = 0.1874 (Rfree = 0.000) for 4445 atoms. Found 12 (33 requested) and removed 26 (16 requested) atoms. Cycle 33: After refmac, R = 0.1782 (Rfree = 0.000) for 4424 atoms. Found 6 (33 requested) and removed 21 (16 requested) atoms. Cycle 34: After refmac, R = 0.1729 (Rfree = 0.000) for 4408 atoms. Found 10 (33 requested) and removed 22 (16 requested) atoms. Cycle 35: After refmac, R = 0.1680 (Rfree = 0.000) for 4394 atoms. Found 9 (33 requested) and removed 18 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.91 3.33 Search for helices and strands: 0 residues in 0 chains, 4504 seeds are put forward Round 1: 242 peptides, 46 chains. Longest chain 13 peptides. Score 0.353 Round 2: 283 peptides, 43 chains. Longest chain 15 peptides. Score 0.501 Round 3: 269 peptides, 40 chains. Longest chain 17 peptides. Score 0.498 Round 4: 279 peptides, 41 chains. Longest chain 16 peptides. Score 0.512 Round 5: 270 peptides, 39 chains. Longest chain 17 peptides. Score 0.512 Taking the results from Round 5 Chains 39, Residues 231, Estimated correctness of the model 0.0 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 10332 restraints for refining 4473 atoms. 9376 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1992 (Rfree = 0.000) for 4473 atoms. Found 22 (33 requested) and removed 27 (16 requested) atoms. Cycle 37: After refmac, R = 0.1826 (Rfree = 0.000) for 4461 atoms. Found 13 (33 requested) and removed 20 (16 requested) atoms. Cycle 38: After refmac, R = 0.1838 (Rfree = 0.000) for 4451 atoms. Found 14 (33 requested) and removed 21 (16 requested) atoms. Cycle 39: After refmac, R = 0.1747 (Rfree = 0.000) for 4443 atoms. Found 11 (33 requested) and removed 20 (16 requested) atoms. Cycle 40: After refmac, R = 0.1711 (Rfree = 0.000) for 4432 atoms. Found 11 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.93 3.35 Search for helices and strands: 0 residues in 0 chains, 4531 seeds are put forward Round 1: 233 peptides, 45 chains. Longest chain 11 peptides. Score 0.339 Round 2: 261 peptides, 45 chains. Longest chain 14 peptides. Score 0.420 Round 3: 267 peptides, 43 chains. Longest chain 13 peptides. Score 0.459 Round 4: 264 peptides, 43 chains. Longest chain 12 peptides. Score 0.451 Round 5: 260 peptides, 43 chains. Longest chain 12 peptides. Score 0.440 Taking the results from Round 3 Chains 43, Residues 224, Estimated correctness of the model 0.0 % 5 chains (22 residues) have been docked in sequence ------------------------------------------------------ 8022 reflections ( 98.42 % complete ) and 10254 restraints for refining 4472 atoms. 9354 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1890 (Rfree = 0.000) for 4472 atoms. Found 22 (33 requested) and removed 32 (16 requested) atoms. Cycle 42: After refmac, R = 0.1779 (Rfree = 0.000) for 4453 atoms. Found 12 (33 requested) and removed 21 (16 requested) atoms. Cycle 43: After refmac, R = 0.1766 (Rfree = 0.000) for 4439 atoms. Found 9 (33 requested) and removed 19 (16 requested) atoms. Cycle 44: After refmac, R = 0.1769 (Rfree = 0.000) for 4427 atoms. Found 7 (33 requested) and removed 16 (16 requested) atoms. Cycle 45: After refmac, R = 0.1787 (Rfree = 0.000) for 4414 atoms. Found 12 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.90 3.32 Search for helices and strands: 0 residues in 0 chains, 4518 seeds are put forward Round 1: 219 peptides, 44 chains. Longest chain 9 peptides. Score 0.309 Round 2: 247 peptides, 41 chains. Longest chain 14 peptides. Score 0.429 Round 3: 248 peptides, 40 chains. Longest chain 16 peptides. Score 0.443 Round 4: 258 peptides, 41 chains. Longest chain 16 peptides. Score 0.458 Round 5: 243 peptides, 41 chains. Longest chain 12 peptides. Score 0.417 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 42, Residues 217, Estimated correctness of the model 0.0 % 4 chains (22 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 1vk3-3_warpNtrace.pdb as input Building loops using Loopy2018 42 chains (217 residues) following loop building 4 chains (22 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8022 reflections ( 98.42 % complete ) and 10245 restraints for refining 4473 atoms. 9359 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1944 (Rfree = 0.000) for 4473 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1875 (Rfree = 0.000) for 4446 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1894 (Rfree = 0.000) for 4429 atoms. Found 0 (33 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1890 (Rfree = 0.000) for 4407 atoms. TimeTaking 62.97