null Tue 25 Dec 19:27:57 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 2h1q-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-3.6-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/2h1q-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-3.6-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 ============================================================ Tue 25 Dec 19:28:07 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/2h1q-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-3.6-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 396 and 0 Target number of residues in the AU: 396 Target solvent content: 0.6615 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.54 Input MTZ file: 2h1q-3.6-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 4320 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: 28.996 3.600 Wilson plot Bfac: 86.03 7323 reflections ( 99.62 % complete ) and 0 restraints for refining 4770 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3437 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3310 (Rfree = 0.000) for 4770 atoms. Found 30 (30 requested) and removed 228 (15 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 4618 seeds are put forward NCS extension: 0 residues added, 4618 seeds are put forward Round 1: 139 peptides, 29 chains. Longest chain 8 peptides. Score 0.246 Round 2: 182 peptides, 35 chains. Longest chain 10 peptides. Score 0.300 Round 3: 212 peptides, 40 chains. Longest chain 10 peptides. Score 0.324 Round 4: 213 peptides, 39 chains. Longest chain 10 peptides. Score 0.339 Round 5: 212 peptides, 38 chains. Longest chain 13 peptides. Score 0.348 Taking the results from Round 5 Chains 38, Residues 174, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 9726 restraints for refining 3916 atoms. 9068 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2739 (Rfree = 0.000) for 3916 atoms. Found 11 (25 requested) and removed 66 (12 requested) atoms. Cycle 2: After refmac, R = 0.2551 (Rfree = 0.000) for 3803 atoms. Found 13 (24 requested) and removed 42 (12 requested) atoms. Cycle 3: After refmac, R = 0.2495 (Rfree = 0.000) for 3744 atoms. Found 12 (24 requested) and removed 25 (12 requested) atoms. Cycle 4: After refmac, R = 0.2440 (Rfree = 0.000) for 3707 atoms. Found 17 (23 requested) and removed 20 (11 requested) atoms. Cycle 5: After refmac, R = 0.2347 (Rfree = 0.000) for 3692 atoms. Found 14 (23 requested) and removed 25 (11 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 3839 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 3858 seeds are put forward Round 1: 184 peptides, 38 chains. Longest chain 7 peptides. Score 0.268 Round 2: 244 peptides, 41 chains. Longest chain 16 peptides. Score 0.398 Round 3: 265 peptides, 43 chains. Longest chain 15 peptides. Score 0.429 Round 4: 258 peptides, 42 chains. Longest chain 14 peptides. Score 0.422 Round 5: 249 peptides, 39 chains. Longest chain 18 peptides. Score 0.433 Taking the results from Round 5 Chains 41, Residues 210, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 8591 restraints for refining 3705 atoms. 7755 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2621 (Rfree = 0.000) for 3705 atoms. Found 23 (23 requested) and removed 51 (11 requested) atoms. Cycle 7: After refmac, R = 0.2541 (Rfree = 0.000) for 3640 atoms. Found 23 (23 requested) and removed 46 (11 requested) atoms. Cycle 8: After refmac, R = 0.2274 (Rfree = 0.000) for 3602 atoms. Found 22 (23 requested) and removed 35 (11 requested) atoms. Cycle 9: After refmac, R = 0.2214 (Rfree = 0.000) for 3575 atoms. Found 20 (23 requested) and removed 30 (11 requested) atoms. Cycle 10: After refmac, R = 0.2196 (Rfree = 0.000) for 3554 atoms. Found 18 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3664 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 3684 seeds are put forward Round 1: 226 peptides, 41 chains. Longest chain 10 peptides. Score 0.351 Round 2: 263 peptides, 40 chains. Longest chain 15 peptides. Score 0.456 Round 3: 251 peptides, 39 chains. Longest chain 15 peptides. Score 0.438 Round 4: 272 peptides, 44 chains. Longest chain 15 peptides. Score 0.435 Round 5: 271 peptides, 44 chains. Longest chain 13 peptides. Score 0.433 Taking the results from Round 2 Chains 40, Residues 223, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 8217 restraints for refining 3650 atoms. 7365 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2195 (Rfree = 0.000) for 3650 atoms. Found 12 (23 requested) and removed 31 (11 requested) atoms. Cycle 12: After refmac, R = 0.2274 (Rfree = 0.000) for 3614 atoms. Found 21 (23 requested) and removed 40 (11 requested) atoms. Cycle 13: After refmac, R = 0.2240 (Rfree = 0.000) for 3587 atoms. Found 16 (23 requested) and removed 24 (11 requested) atoms. Cycle 14: After refmac, R = 0.2166 (Rfree = 0.000) for 3575 atoms. Found 20 (22 requested) and removed 25 (11 requested) atoms. Cycle 15: After refmac, R = 0.1825 (Rfree = 0.000) for 3565 atoms. Found 5 (22 requested) and removed 21 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3668 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 3686 seeds are put forward Round 1: 208 peptides, 40 chains. Longest chain 11 peptides. Score 0.313 Round 2: 237 peptides, 37 chains. Longest chain 12 peptides. Score 0.425 Round 3: 247 peptides, 39 chains. Longest chain 13 peptides. Score 0.428 Round 4: 260 peptides, 38 chains. Longest chain 15 peptides. Score 0.470 Round 5: 257 peptides, 36 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 36, Residues 221, Estimated correctness of the model 0.0 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 8748 restraints for refining 3859 atoms. 7835 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2190 (Rfree = 0.000) for 3859 atoms. Found 17 (24 requested) and removed 44 (12 requested) atoms. Cycle 17: After refmac, R = 0.1992 (Rfree = 0.000) for 3811 atoms. Found 12 (24 requested) and removed 38 (12 requested) atoms. Cycle 18: After refmac, R = 0.1935 (Rfree = 0.000) for 3770 atoms. Found 10 (24 requested) and removed 25 (12 requested) atoms. Cycle 19: After refmac, R = 0.1874 (Rfree = 0.000) for 3750 atoms. Found 8 (24 requested) and removed 21 (12 requested) atoms. Cycle 20: After refmac, R = 0.1835 (Rfree = 0.000) for 3728 atoms. Found 10 (23 requested) and removed 20 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3822 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 3837 seeds are put forward Round 1: 209 peptides, 37 chains. Longest chain 17 peptides. Score 0.351 Round 2: 234 peptides, 39 chains. Longest chain 11 peptides. Score 0.395 Round 3: 252 peptides, 36 chains. Longest chain 18 peptides. Score 0.472 Round 4: 243 peptides, 33 chains. Longest chain 20 peptides. Score 0.483 Round 5: 246 peptides, 37 chains. Longest chain 20 peptides. Score 0.447 Taking the results from Round 4 Chains 34, Residues 210, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 8644 restraints for refining 3838 atoms. 7794 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2164 (Rfree = 0.000) for 3838 atoms. Found 24 (24 requested) and removed 43 (12 requested) atoms. Cycle 22: After refmac, R = 0.2009 (Rfree = 0.000) for 3805 atoms. Found 14 (24 requested) and removed 27 (12 requested) atoms. Cycle 23: After refmac, R = 0.2035 (Rfree = 0.000) for 3785 atoms. Found 21 (24 requested) and removed 24 (12 requested) atoms. Cycle 24: After refmac, R = 0.1934 (Rfree = 0.000) for 3774 atoms. Found 13 (24 requested) and removed 19 (12 requested) atoms. Cycle 25: After refmac, R = 0.1746 (Rfree = 0.000) for 3761 atoms. Found 6 (24 requested) and removed 17 (12 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.44 Search for helices and strands: 0 residues in 0 chains, 3850 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 3871 seeds are put forward Round 1: 198 peptides, 39 chains. Longest chain 10 peptides. Score 0.296 Round 2: 222 peptides, 36 chains. Longest chain 13 peptides. Score 0.398 Round 3: 228 peptides, 36 chains. Longest chain 16 peptides. Score 0.413 Round 4: 226 peptides, 37 chains. Longest chain 18 peptides. Score 0.397 Round 5: 228 peptides, 35 chains. Longest chain 20 peptides. Score 0.424 Taking the results from Round 5 Chains 35, Residues 193, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 9040 restraints for refining 3916 atoms. 8247 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2171 (Rfree = 0.000) for 3916 atoms. Found 25 (25 requested) and removed 41 (12 requested) atoms. Cycle 27: After refmac, R = 0.2044 (Rfree = 0.000) for 3880 atoms. Found 19 (25 requested) and removed 31 (12 requested) atoms. Cycle 28: After refmac, R = 0.1968 (Rfree = 0.000) for 3860 atoms. Found 19 (24 requested) and removed 19 (12 requested) atoms. Cycle 29: After refmac, R = 0.1951 (Rfree = 0.000) for 3855 atoms. Found 18 (24 requested) and removed 21 (12 requested) atoms. Cycle 30: After refmac, R = 0.1860 (Rfree = 0.000) for 3847 atoms. Found 13 (24 requested) and removed 19 (12 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.61 3.42 Search for helices and strands: 0 residues in 0 chains, 3975 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 4000 seeds are put forward Round 1: 187 peptides, 39 chains. Longest chain 11 peptides. Score 0.264 Round 2: 195 peptides, 36 chains. Longest chain 10 peptides. Score 0.325 Round 3: 197 peptides, 32 chains. Longest chain 14 peptides. Score 0.378 Round 4: 211 peptides, 37 chains. Longest chain 13 peptides. Score 0.357 Round 5: 212 peptides, 36 chains. Longest chain 13 peptides. Score 0.371 Taking the results from Round 3 Chains 32, Residues 165, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 9299 restraints for refining 3916 atoms. 8671 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2027 (Rfree = 0.000) for 3916 atoms. Found 25 (25 requested) and removed 32 (12 requested) atoms. Cycle 32: After refmac, R = 0.2123 (Rfree = 0.000) for 3904 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 33: After refmac, R = 0.1794 (Rfree = 0.000) for 3884 atoms. Found 20 (24 requested) and removed 20 (12 requested) atoms. Cycle 34: After refmac, R = 0.1740 (Rfree = 0.000) for 3879 atoms. Found 24 (24 requested) and removed 19 (12 requested) atoms. Cycle 35: After refmac, R = 0.1444 (Rfree = 0.000) for 3875 atoms. Found 2 (24 requested) and removed 14 (12 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3958 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 3972 seeds are put forward Round 1: 185 peptides, 36 chains. Longest chain 9 peptides. Score 0.296 Round 2: 202 peptides, 36 chains. Longest chain 12 peptides. Score 0.344 Round 3: 223 peptides, 38 chains. Longest chain 14 peptides. Score 0.377 Round 4: 228 peptides, 40 chains. Longest chain 11 peptides. Score 0.368 Round 5: 218 peptides, 39 chains. Longest chain 11 peptides. Score 0.352 Taking the results from Round 3 Chains 38, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 9286 restraints for refining 3914 atoms. 8584 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1950 (Rfree = 0.000) for 3914 atoms. Found 25 (25 requested) and removed 29 (12 requested) atoms. Cycle 37: After refmac, R = 0.1880 (Rfree = 0.000) for 3898 atoms. Found 25 (25 requested) and removed 22 (12 requested) atoms. Cycle 38: After refmac, R = 0.1829 (Rfree = 0.000) for 3887 atoms. Found 18 (25 requested) and removed 22 (12 requested) atoms. Cycle 39: After refmac, R = 0.1704 (Rfree = 0.000) for 3875 atoms. Found 16 (24 requested) and removed 22 (12 requested) atoms. Cycle 40: After refmac, R = 0.1772 (Rfree = 0.000) for 3861 atoms. Found 22 (24 requested) and removed 24 (12 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 3982 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 3995 seeds are put forward Round 1: 169 peptides, 36 chains. Longest chain 9 peptides. Score 0.248 Round 2: 197 peptides, 37 chains. Longest chain 9 peptides. Score 0.318 Round 3: 200 peptides, 38 chains. Longest chain 9 peptides. Score 0.314 Round 4: 207 peptides, 36 chains. Longest chain 12 peptides. Score 0.358 Round 5: 195 peptides, 37 chains. Longest chain 10 peptides. Score 0.312 Taking the results from Round 4 Chains 36, Residues 171, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 7323 reflections ( 99.62 % complete ) and 9322 restraints for refining 3914 atoms. 8674 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1901 (Rfree = 0.000) for 3914 atoms. Found 25 (25 requested) and removed 33 (12 requested) atoms. Cycle 42: After refmac, R = 0.1768 (Rfree = 0.000) for 3892 atoms. Found 25 (25 requested) and removed 23 (12 requested) atoms. Cycle 43: After refmac, R = 0.1678 (Rfree = 0.000) for 3884 atoms. Found 17 (24 requested) and removed 22 (12 requested) atoms. Cycle 44: After refmac, R = 0.1730 (Rfree = 0.000) for 3872 atoms. Found 24 (24 requested) and removed 20 (12 requested) atoms. Cycle 45: After refmac, R = 0.1595 (Rfree = 0.000) for 3874 atoms. Found 15 (24 requested) and removed 16 (12 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.59 3.40 Search for helices and strands: 0 residues in 0 chains, 3975 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 3991 seeds are put forward Round 1: 179 peptides, 38 chains. Longest chain 9 peptides. Score 0.253 Round 2: 215 peptides, 41 chains. Longest chain 10 peptides. Score 0.321 Round 3: 211 peptides, 36 chains. Longest chain 12 peptides. Score 0.369 Round 4: 215 peptides, 38 chains. Longest chain 12 peptides. Score 0.356 Round 5: 217 peptides, 38 chains. Longest chain 10 peptides. Score 0.361 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 175, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7323 reflections ( 99.62 % complete ) and 9312 restraints for refining 3914 atoms. 8648 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1788 (Rfree = 0.000) for 3914 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 47: After refmac, R = 0.1860 (Rfree = 0.000) for 3890 atoms. Found 0 (25 requested) and removed 12 (12 requested) atoms. Cycle 48: After refmac, R = 0.1786 (Rfree = 0.000) for 3872 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Cycle 49: After refmac, R = 0.1817 (Rfree = 0.000) for 3853 atoms. Found 0 (24 requested) and removed 12 (12 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:35:07 GMT 2018 Job finished. TimeTaking 67.17 Used memory is bytes: 12328424