null Mon 24 Dec 07:37:44 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2h1q-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2h1q-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2h1q-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:37:49 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/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-noncs/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 415 and 0 Target number of residues in the AU: 415 Target solvent content: 0.6452 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-3.2-parrot-noncs.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-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 4320 target number of atoms Had to go as low as 0.70 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 3.200 Wilson plot Bfac: 74.70 10405 reflections ( 99.63 % complete ) and 0 restraints for refining 4825 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3375 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2592 (Rfree = 0.000) for 4825 atoms. Found 20 (43 requested) and removed 35 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4880 seeds are put forward NCS extension: 0 residues added, 4880 seeds are put forward Round 1: 203 peptides, 40 chains. Longest chain 9 peptides. Score 0.299 Round 2: 251 peptides, 41 chains. Longest chain 13 peptides. Score 0.416 Round 3: 267 peptides, 39 chains. Longest chain 14 peptides. Score 0.476 Round 4: 282 peptides, 43 chains. Longest chain 19 peptides. Score 0.470 Round 5: 298 peptides, 37 chains. Longest chain 21 peptides. Score 0.564 Taking the results from Round 5 Chains 37, Residues 261, Estimated correctness of the model 31.0 % 2 chains (15 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8636 restraints for refining 3830 atoms. 7583 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2787 (Rfree = 0.000) for 3830 atoms. Found 29 (34 requested) and removed 38 (17 requested) atoms. Cycle 2: After refmac, R = 0.2560 (Rfree = 0.000) for 3792 atoms. Found 13 (34 requested) and removed 29 (17 requested) atoms. Cycle 3: After refmac, R = 0.2509 (Rfree = 0.000) for 3754 atoms. Found 8 (33 requested) and removed 24 (16 requested) atoms. Cycle 4: After refmac, R = 0.2450 (Rfree = 0.000) for 3732 atoms. Found 5 (33 requested) and removed 20 (16 requested) atoms. Cycle 5: After refmac, R = 0.2534 (Rfree = 0.000) for 3708 atoms. Found 11 (33 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3803 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3834 seeds are put forward Round 1: 291 peptides, 47 chains. Longest chain 18 peptides. Score 0.450 Round 2: 317 peptides, 43 chains. Longest chain 22 peptides. Score 0.547 Round 3: 308 peptides, 36 chains. Longest chain 22 peptides. Score 0.593 Round 4: 305 peptides, 37 chains. Longest chain 29 peptides. Score 0.578 Round 5: 310 peptides, 38 chains. Longest chain 23 peptides. Score 0.578 Taking the results from Round 3 Chains 36, Residues 272, Estimated correctness of the model 39.2 % 2 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8214 restraints for refining 3760 atoms. 7134 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2665 (Rfree = 0.000) for 3760 atoms. Found 33 (33 requested) and removed 43 (16 requested) atoms. Cycle 7: After refmac, R = 0.2467 (Rfree = 0.000) for 3741 atoms. Found 13 (33 requested) and removed 29 (16 requested) atoms. Cycle 8: After refmac, R = 0.2409 (Rfree = 0.000) for 3716 atoms. Found 11 (33 requested) and removed 18 (16 requested) atoms. Cycle 9: After refmac, R = 0.2277 (Rfree = 0.000) for 3707 atoms. Found 7 (33 requested) and removed 18 (16 requested) atoms. Cycle 10: After refmac, R = 0.2252 (Rfree = 0.000) for 3683 atoms. Found 4 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3760 seeds are put forward NCS extension: 28 residues added (4 deleted due to clashes), 3788 seeds are put forward Round 1: 269 peptides, 42 chains. Longest chain 14 peptides. Score 0.449 Round 2: 296 peptides, 40 chains. Longest chain 17 peptides. Score 0.531 Round 3: 292 peptides, 41 chains. Longest chain 21 peptides. Score 0.513 Round 4: 296 peptides, 31 chains. Longest chain 32 peptides. Score 0.614 Round 5: 311 peptides, 39 chains. Longest chain 21 peptides. Score 0.571 Taking the results from Round 4 Chains 36, Residues 265, Estimated correctness of the model 44.8 % 3 chains (59 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8011 restraints for refining 3859 atoms. 6774 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2532 (Rfree = 0.000) for 3859 atoms. Found 34 (34 requested) and removed 55 (17 requested) atoms. Cycle 12: After refmac, R = 0.2382 (Rfree = 0.000) for 3815 atoms. Found 17 (34 requested) and removed 33 (17 requested) atoms. Cycle 13: After refmac, R = 0.2237 (Rfree = 0.000) for 3790 atoms. Found 6 (34 requested) and removed 25 (17 requested) atoms. Cycle 14: After refmac, R = 0.2263 (Rfree = 0.000) for 3764 atoms. Found 11 (33 requested) and removed 24 (16 requested) atoms. Cycle 15: After refmac, R = 0.2233 (Rfree = 0.000) for 3739 atoms. Found 14 (33 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3834 seeds are put forward NCS extension: 31 residues added (3 deleted due to clashes), 3865 seeds are put forward Round 1: 271 peptides, 43 chains. Longest chain 16 peptides. Score 0.444 Round 2: 272 peptides, 34 chains. Longest chain 28 peptides. Score 0.538 Round 3: 287 peptides, 37 chains. Longest chain 20 peptides. Score 0.541 Round 4: 288 peptides, 36 chains. Longest chain 26 peptides. Score 0.552 Round 5: 291 peptides, 35 chains. Longest chain 24 peptides. Score 0.568 Taking the results from Round 5 Chains 37, Residues 256, Estimated correctness of the model 32.1 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8497 restraints for refining 3871 atoms. 7442 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2459 (Rfree = 0.000) for 3871 atoms. Found 33 (34 requested) and removed 28 (17 requested) atoms. Cycle 17: After refmac, R = 0.2251 (Rfree = 0.000) for 3866 atoms. Found 16 (34 requested) and removed 22 (17 requested) atoms. Cycle 18: After refmac, R = 0.2202 (Rfree = 0.000) for 3848 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 19: After refmac, R = 0.2149 (Rfree = 0.000) for 3831 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 20: After refmac, R = 0.2143 (Rfree = 0.000) for 3814 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3896 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3915 seeds are put forward Round 1: 239 peptides, 36 chains. Longest chain 18 peptides. Score 0.441 Round 2: 280 peptides, 37 chains. Longest chain 23 peptides. Score 0.525 Round 3: 297 peptides, 37 chains. Longest chain 36 peptides. Score 0.561 Round 4: 297 peptides, 39 chains. Longest chain 19 peptides. Score 0.543 Round 5: 294 peptides, 35 chains. Longest chain 28 peptides. Score 0.574 Taking the results from Round 5 Chains 37, Residues 259, Estimated correctness of the model 33.9 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8397 restraints for refining 3943 atoms. 7205 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2497 (Rfree = 0.000) for 3943 atoms. Found 31 (35 requested) and removed 28 (17 requested) atoms. Cycle 22: After refmac, R = 0.2383 (Rfree = 0.000) for 3929 atoms. Found 17 (35 requested) and removed 24 (17 requested) atoms. Cycle 23: After refmac, R = 0.2258 (Rfree = 0.000) for 3909 atoms. Found 12 (35 requested) and removed 25 (17 requested) atoms. Cycle 24: After refmac, R = 0.2299 (Rfree = 0.000) for 3886 atoms. Found 16 (34 requested) and removed 18 (17 requested) atoms. Cycle 25: After refmac, R = 0.2123 (Rfree = 0.000) for 3878 atoms. Found 8 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3985 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 4019 seeds are put forward Round 1: 268 peptides, 45 chains. Longest chain 23 peptides. Score 0.415 Round 2: 296 peptides, 43 chains. Longest chain 23 peptides. Score 0.502 Round 3: 288 peptides, 40 chains. Longest chain 18 peptides. Score 0.514 Round 4: 279 peptides, 40 chains. Longest chain 23 peptides. Score 0.493 Round 5: 296 peptides, 38 chains. Longest chain 25 peptides. Score 0.550 Taking the results from Round 5 Chains 39, Residues 258, Estimated correctness of the model 26.9 % 2 chains (37 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8748 restraints for refining 3943 atoms. 7606 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2444 (Rfree = 0.000) for 3943 atoms. Found 24 (35 requested) and removed 28 (17 requested) atoms. Cycle 27: After refmac, R = 0.2192 (Rfree = 0.000) for 3932 atoms. Found 16 (35 requested) and removed 23 (17 requested) atoms. Cycle 28: After refmac, R = 0.2222 (Rfree = 0.000) for 3916 atoms. Found 9 (35 requested) and removed 24 (17 requested) atoms. Cycle 29: After refmac, R = 0.2087 (Rfree = 0.000) for 3890 atoms. Found 5 (35 requested) and removed 26 (17 requested) atoms. Cycle 30: After refmac, R = 0.2151 (Rfree = 0.000) for 3857 atoms. Found 9 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3984 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 4006 seeds are put forward Round 1: 240 peptides, 38 chains. Longest chain 20 peptides. Score 0.421 Round 2: 270 peptides, 38 chains. Longest chain 19 peptides. Score 0.493 Round 3: 275 peptides, 37 chains. Longest chain 22 peptides. Score 0.515 Round 4: 283 peptides, 37 chains. Longest chain 23 peptides. Score 0.532 Round 5: 276 peptides, 38 chains. Longest chain 17 peptides. Score 0.507 Taking the results from Round 4 Chains 39, Residues 246, Estimated correctness of the model 21.4 % 4 chains (22 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8892 restraints for refining 3944 atoms. 7886 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2324 (Rfree = 0.000) for 3944 atoms. Found 26 (35 requested) and removed 39 (17 requested) atoms. Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 3917 atoms. Found 16 (35 requested) and removed 23 (17 requested) atoms. Cycle 33: After refmac, R = 0.2071 (Rfree = 0.000) for 3904 atoms. Found 12 (35 requested) and removed 22 (17 requested) atoms. Cycle 34: After refmac, R = 0.1910 (Rfree = 0.000) for 3885 atoms. Found 7 (34 requested) and removed 24 (17 requested) atoms. Cycle 35: After refmac, R = 0.1936 (Rfree = 0.000) for 3865 atoms. Found 10 (34 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3972 seeds are put forward NCS extension: 27 residues added (0 deleted due to clashes), 3999 seeds are put forward Round 1: 233 peptides, 37 chains. Longest chain 15 peptides. Score 0.415 Round 2: 268 peptides, 40 chains. Longest chain 22 peptides. Score 0.468 Round 3: 269 peptides, 38 chains. Longest chain 19 peptides. Score 0.491 Round 4: 274 peptides, 39 chains. Longest chain 23 peptides. Score 0.492 Round 5: 260 peptides, 39 chains. Longest chain 14 peptides. Score 0.459 Taking the results from Round 4 Chains 39, Residues 235, Estimated correctness of the model 8.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8904 restraints for refining 3944 atoms. 8003 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2134 (Rfree = 0.000) for 3944 atoms. Found 19 (35 requested) and removed 30 (17 requested) atoms. Cycle 37: After refmac, R = 0.2303 (Rfree = 0.000) for 3925 atoms. Found 26 (35 requested) and removed 27 (17 requested) atoms. Cycle 38: After refmac, R = 0.2104 (Rfree = 0.000) for 3917 atoms. Found 18 (35 requested) and removed 30 (17 requested) atoms. Cycle 39: After refmac, R = 0.1867 (Rfree = 0.000) for 3902 atoms. Found 2 (35 requested) and removed 19 (17 requested) atoms. Cycle 40: After refmac, R = 0.1817 (Rfree = 0.000) for 3881 atoms. Found 3 (34 requested) and removed 22 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3964 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3983 seeds are put forward Round 1: 214 peptides, 37 chains. Longest chain 14 peptides. Score 0.365 Round 2: 244 peptides, 34 chains. Longest chain 17 peptides. Score 0.475 Round 3: 253 peptides, 39 chains. Longest chain 21 peptides. Score 0.443 Round 4: 249 peptides, 37 chains. Longest chain 19 peptides. Score 0.454 Round 5: 244 peptides, 35 chains. Longest chain 17 peptides. Score 0.464 Taking the results from Round 2 Chains 34, Residues 210, Estimated correctness of the model 3.1 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8888 restraints for refining 3944 atoms. 8058 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2270 (Rfree = 0.000) for 3944 atoms. Found 34 (35 requested) and removed 28 (17 requested) atoms. Cycle 42: After refmac, R = 0.1927 (Rfree = 0.000) for 3936 atoms. Found 11 (35 requested) and removed 26 (17 requested) atoms. Cycle 43: After refmac, R = 0.1783 (Rfree = 0.000) for 3915 atoms. Found 7 (35 requested) and removed 20 (17 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 3900 atoms. Found 13 (35 requested) and removed 22 (17 requested) atoms. Cycle 45: After refmac, R = 0.1738 (Rfree = 0.000) for 3890 atoms. Found 7 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3976 seeds are put forward NCS extension: 18 residues added (5 deleted due to clashes), 3994 seeds are put forward Round 1: 205 peptides, 37 chains. Longest chain 20 peptides. Score 0.340 Round 2: 227 peptides, 33 chains. Longest chain 21 peptides. Score 0.444 Round 3: 239 peptides, 35 chains. Longest chain 21 peptides. Score 0.452 Round 4: 243 peptides, 31 chains. Longest chain 23 peptides. Score 0.504 Round 5: 237 peptides, 32 chains. Longest chain 17 peptides. Score 0.479 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 35, Residues 212, Estimated correctness of the model 12.6 % 3 chains (34 residues) have been docked in sequence Sequence coverage is 15 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input Building loops using Loopy2018 35 chains (212 residues) following loop building 3 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10405 reflections ( 99.63 % complete ) and 8640 restraints for refining 3944 atoms. 7699 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2090 (Rfree = 0.000) for 3944 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2252 (Rfree = 0.000) for 3919 atoms. Found 0 (35 requested) and removed 12 (17 requested) atoms. Cycle 48: After refmac, R = 0.2060 (Rfree = 0.000) for 3904 atoms. Found 0 (35 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.1996 (Rfree = 0.000) for 3884 atoms. Found 0 (34 requested) and removed 6 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:29:23 GMT 2018 Job finished. TimeTaking 51.65 Used memory is bytes: 16184520