null Sun 23 Dec 22:23:05 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-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-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 22:23:14 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-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 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-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-3.2-parrot-hancs.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 4813 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3305 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2487 (Rfree = 0.000) for 4813 atoms. Found 18 (43 requested) and removed 40 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4867 seeds are put forward NCS extension: 0 residues added, 4867 seeds are put forward Round 1: 236 peptides, 42 chains. Longest chain 13 peptides. Score 0.366 Round 2: 289 peptides, 37 chains. Longest chain 19 peptides. Score 0.545 Round 3: 276 peptides, 34 chains. Longest chain 23 peptides. Score 0.546 Round 4: 287 peptides, 36 chains. Longest chain 24 peptides. Score 0.550 Round 5: 296 peptides, 34 chains. Longest chain 22 peptides. Score 0.587 Taking the results from Round 5 Chains 36, Residues 262, Estimated correctness of the model 37.5 % 4 chains (49 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8652 restraints for refining 3942 atoms. 7461 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2826 (Rfree = 0.000) for 3942 atoms. Found 35 (35 requested) and removed 28 (17 requested) atoms. Cycle 2: After refmac, R = 0.2602 (Rfree = 0.000) for 3923 atoms. Found 8 (35 requested) and removed 24 (17 requested) atoms. Cycle 3: After refmac, R = 0.2555 (Rfree = 0.000) for 3875 atoms. Found 12 (35 requested) and removed 19 (17 requested) atoms. Cycle 4: After refmac, R = 0.2632 (Rfree = 0.000) for 3848 atoms. Found 11 (34 requested) and removed 17 (17 requested) atoms. Cycle 5: After refmac, R = 0.2500 (Rfree = 0.000) for 3826 atoms. Found 9 (34 requested) and removed 23 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.34 3.17 Search for helices and strands: 0 residues in 0 chains, 3935 seeds are put forward NCS extension: 0 residues added, 3935 seeds are put forward Round 1: 240 peptides, 36 chains. Longest chain 14 peptides. Score 0.443 Round 2: 282 peptides, 36 chains. Longest chain 19 peptides. Score 0.540 Round 3: 282 peptides, 37 chains. Longest chain 16 peptides. Score 0.530 Round 4: 297 peptides, 37 chains. Longest chain 19 peptides. Score 0.561 Round 5: 299 peptides, 39 chains. Longest chain 20 peptides. Score 0.547 Taking the results from Round 4 Chains 39, Residues 260, Estimated correctness of the model 30.1 % 3 chains (23 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8495 restraints for refining 3796 atoms. 7409 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2802 (Rfree = 0.000) for 3796 atoms. Found 34 (34 requested) and removed 29 (17 requested) atoms. Cycle 7: After refmac, R = 0.2519 (Rfree = 0.000) for 3798 atoms. Found 19 (34 requested) and removed 19 (17 requested) atoms. Cycle 8: After refmac, R = 0.2456 (Rfree = 0.000) for 3790 atoms. Found 10 (34 requested) and removed 18 (17 requested) atoms. Cycle 9: After refmac, R = 0.2380 (Rfree = 0.000) for 3776 atoms. Found 8 (33 requested) and removed 17 (16 requested) atoms. Cycle 10: After refmac, R = 0.2353 (Rfree = 0.000) for 3761 atoms. Found 4 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3873 seeds are put forward NCS extension: 17 residues added (4 deleted due to clashes), 3890 seeds are put forward Round 1: 290 peptides, 47 chains. Longest chain 15 peptides. Score 0.447 Round 2: 292 peptides, 34 chains. Longest chain 20 peptides. Score 0.579 Round 3: 300 peptides, 37 chains. Longest chain 30 peptides. Score 0.568 Round 4: 298 peptides, 37 chains. Longest chain 20 peptides. Score 0.564 Round 5: 290 peptides, 37 chains. Longest chain 25 peptides. Score 0.547 Taking the results from Round 2 Chains 35, Residues 258, Estimated correctness of the model 35.3 % 5 chains (60 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8159 restraints for refining 3851 atoms. 6939 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2572 (Rfree = 0.000) for 3851 atoms. Found 22 (34 requested) and removed 36 (17 requested) atoms. Cycle 12: After refmac, R = 0.2494 (Rfree = 0.000) for 3823 atoms. Found 17 (34 requested) and removed 30 (17 requested) atoms. Cycle 13: After refmac, R = 0.2297 (Rfree = 0.000) for 3787 atoms. Found 8 (34 requested) and removed 25 (17 requested) atoms. Cycle 14: After refmac, R = 0.2194 (Rfree = 0.000) for 3752 atoms. Found 6 (33 requested) and removed 23 (16 requested) atoms. Cycle 15: After refmac, R = 0.2157 (Rfree = 0.000) for 3730 atoms. Found 5 (33 requested) and removed 23 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3816 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3829 seeds are put forward Round 1: 255 peptides, 35 chains. Longest chain 15 peptides. Score 0.490 Round 2: 289 peptides, 40 chains. Longest chain 17 peptides. Score 0.516 Round 3: 291 peptides, 38 chains. Longest chain 39 peptides. Score 0.539 Round 4: 277 peptides, 38 chains. Longest chain 25 peptides. Score 0.509 Round 5: 294 peptides, 40 chains. Longest chain 28 peptides. Score 0.527 Taking the results from Round 3 Chains 39, Residues 253, Estimated correctness of the model 23.6 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8628 restraints for refining 3842 atoms. 7588 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2484 (Rfree = 0.000) for 3842 atoms. Found 34 (34 requested) and removed 27 (17 requested) atoms. Cycle 17: After refmac, R = 0.2346 (Rfree = 0.000) for 3848 atoms. Found 22 (34 requested) and removed 25 (17 requested) atoms. Cycle 18: After refmac, R = 0.2187 (Rfree = 0.000) for 3827 atoms. Found 9 (34 requested) and removed 19 (17 requested) atoms. Cycle 19: After refmac, R = 0.2149 (Rfree = 0.000) for 3810 atoms. Found 5 (34 requested) and removed 21 (17 requested) atoms. Cycle 20: After refmac, R = 0.2372 (Rfree = 0.000) for 3791 atoms. Found 34 (34 requested) and removed 25 (17 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3946 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3982 seeds are put forward Round 1: 257 peptides, 41 chains. Longest chain 25 peptides. Score 0.431 Round 2: 291 peptides, 43 chains. Longest chain 21 peptides. Score 0.490 Round 3: 276 peptides, 39 chains. Longest chain 20 peptides. Score 0.497 Round 4: 265 peptides, 38 chains. Longest chain 16 peptides. Score 0.482 Round 5: 267 peptides, 36 chains. Longest chain 14 peptides. Score 0.507 Taking the results from Round 5 Chains 36, Residues 231, Estimated correctness of the model 13.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8996 restraints for refining 3875 atoms. 8108 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2469 (Rfree = 0.000) for 3875 atoms. Found 21 (34 requested) and removed 36 (17 requested) atoms. Cycle 22: After refmac, R = 0.2177 (Rfree = 0.000) for 3844 atoms. Found 16 (34 requested) and removed 21 (17 requested) atoms. Cycle 23: After refmac, R = 0.2061 (Rfree = 0.000) for 3824 atoms. Found 9 (34 requested) and removed 20 (17 requested) atoms. Cycle 24: After refmac, R = 0.1964 (Rfree = 0.000) for 3802 atoms. Found 12 (34 requested) and removed 19 (17 requested) atoms. Cycle 25: After refmac, R = 0.1832 (Rfree = 0.000) for 3783 atoms. Found 6 (34 requested) and removed 20 (17 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 3906 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 3918 seeds are put forward Round 1: 262 peptides, 39 chains. Longest chain 28 peptides. Score 0.464 Round 2: 294 peptides, 40 chains. Longest chain 28 peptides. Score 0.527 Round 3: 300 peptides, 41 chains. Longest chain 30 peptides. Score 0.530 Round 4: 300 peptides, 38 chains. Longest chain 24 peptides. Score 0.558 Round 5: 306 peptides, 37 chains. Longest chain 22 peptides. Score 0.580 Taking the results from Round 5 Chains 39, Residues 269, Estimated correctness of the model 35.6 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8418 restraints for refining 3867 atoms. 7336 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2270 (Rfree = 0.000) for 3867 atoms. Found 21 (34 requested) and removed 34 (17 requested) atoms. Cycle 27: After refmac, R = 0.2080 (Rfree = 0.000) for 3846 atoms. Found 7 (34 requested) and removed 20 (17 requested) atoms. Cycle 28: After refmac, R = 0.2022 (Rfree = 0.000) for 3826 atoms. Found 4 (34 requested) and removed 18 (17 requested) atoms. Cycle 29: After refmac, R = 0.1990 (Rfree = 0.000) for 3806 atoms. Found 5 (34 requested) and removed 20 (17 requested) atoms. Cycle 30: After refmac, R = 0.1984 (Rfree = 0.000) for 3785 atoms. Found 11 (34 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 3.13 Search for helices and strands: 0 residues in 0 chains, 3884 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3908 seeds are put forward Round 1: 275 peptides, 44 chains. Longest chain 20 peptides. Score 0.443 Round 2: 294 peptides, 41 chains. Longest chain 19 peptides. Score 0.517 Round 3: 279 peptides, 39 chains. Longest chain 22 peptides. Score 0.503 Round 4: 286 peptides, 37 chains. Longest chain 23 peptides. Score 0.538 Round 5: 288 peptides, 42 chains. Longest chain 22 peptides. Score 0.494 Taking the results from Round 4 Chains 37, Residues 249, Estimated correctness of the model 23.3 % 2 chains (28 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8676 restraints for refining 3944 atoms. 7599 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2366 (Rfree = 0.000) for 3944 atoms. Found 31 (35 requested) and removed 26 (17 requested) atoms. Cycle 32: After refmac, R = 0.2173 (Rfree = 0.000) for 3944 atoms. Found 8 (35 requested) and removed 29 (17 requested) atoms. Cycle 33: After refmac, R = 0.2109 (Rfree = 0.000) for 3921 atoms. Found 4 (35 requested) and removed 19 (17 requested) atoms. Cycle 34: After refmac, R = 0.2062 (Rfree = 0.000) for 3901 atoms. Found 6 (35 requested) and removed 17 (17 requested) atoms. Cycle 35: After refmac, R = 0.2020 (Rfree = 0.000) for 3886 atoms. Found 7 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3990 seeds are put forward NCS extension: 22 residues added (4 deleted due to clashes), 4012 seeds are put forward Round 1: 243 peptides, 42 chains. Longest chain 21 peptides. Score 0.384 Round 2: 265 peptides, 40 chains. Longest chain 13 peptides. Score 0.461 Round 3: 267 peptides, 34 chains. Longest chain 24 peptides. Score 0.527 Round 4: 277 peptides, 36 chains. Longest chain 21 peptides. Score 0.529 Round 5: 290 peptides, 38 chains. Longest chain 27 peptides. Score 0.537 Taking the results from Round 5 Chains 41, Residues 252, Estimated correctness of the model 23.0 % 3 chains (46 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8498 restraints for refining 3944 atoms. 7341 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2386 (Rfree = 0.000) for 3944 atoms. Found 27 (35 requested) and removed 29 (17 requested) atoms. Cycle 37: After refmac, R = 0.2169 (Rfree = 0.000) for 3934 atoms. Found 9 (35 requested) and removed 17 (17 requested) atoms. Cycle 38: After refmac, R = 0.2092 (Rfree = 0.000) for 3922 atoms. Found 10 (35 requested) and removed 18 (17 requested) atoms. Cycle 39: After refmac, R = 0.2054 (Rfree = 0.000) for 3913 atoms. Found 6 (35 requested) and removed 17 (17 requested) atoms. Cycle 40: After refmac, R = 0.2043 (Rfree = 0.000) for 3898 atoms. Found 11 (35 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 4001 seeds are put forward NCS extension: 22 residues added (5 deleted due to clashes), 4023 seeds are put forward Round 1: 228 peptides, 42 chains. Longest chain 16 peptides. Score 0.345 Round 2: 261 peptides, 38 chains. Longest chain 22 peptides. Score 0.472 Round 3: 281 peptides, 39 chains. Longest chain 24 peptides. Score 0.508 Round 4: 267 peptides, 36 chains. Longest chain 24 peptides. Score 0.507 Round 5: 259 peptides, 33 chains. Longest chain 23 peptides. Score 0.519 Taking the results from Round 5 Chains 35, Residues 226, Estimated correctness of the model 17.4 % 2 chains (36 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8758 restraints for refining 3944 atoms. 7744 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2369 (Rfree = 0.000) for 3944 atoms. Found 28 (35 requested) and removed 25 (17 requested) atoms. Cycle 42: After refmac, R = 0.2154 (Rfree = 0.000) for 3941 atoms. Found 1 (35 requested) and removed 18 (17 requested) atoms. Cycle 43: After refmac, R = 0.2107 (Rfree = 0.000) for 3921 atoms. Found 7 (35 requested) and removed 17 (17 requested) atoms. Cycle 44: After refmac, R = 0.2055 (Rfree = 0.000) for 3908 atoms. Found 4 (35 requested) and removed 18 (17 requested) atoms. Cycle 45: After refmac, R = 0.2018 (Rfree = 0.000) for 3891 atoms. Found 3 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 4009 seeds are put forward NCS extension: 24 residues added (3 deleted due to clashes), 4033 seeds are put forward Round 1: 223 peptides, 38 chains. Longest chain 20 peptides. Score 0.377 Round 2: 229 peptides, 31 chains. Longest chain 23 peptides. Score 0.471 Round 3: 223 peptides, 29 chains. Longest chain 32 peptides. Score 0.479 Round 4: 237 peptides, 34 chains. Longest chain 17 peptides. Score 0.458 Round 5: 241 peptides, 30 chains. Longest chain 24 peptides. Score 0.510 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 211, Estimated correctness of the model 14.5 % 2 chains (28 residues) have been docked in sequence Sequence coverage is 13 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 101 A and 109 A 30 chains (214 residues) following loop building 1 chains (35 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10405 reflections ( 99.63 % complete ) and 8626 restraints for refining 3944 atoms. 7711 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2385 (Rfree = 0.000) for 3944 atoms. Found 0 (35 requested) and removed 5 (17 requested) atoms. Cycle 47: After refmac, R = 0.2239 (Rfree = 0.000) for 3928 atoms. Found 0 (35 requested) and removed 4 (17 requested) atoms. Cycle 48: After refmac, R = 0.2309 (Rfree = 0.000) for 3920 atoms. Found 0 (35 requested) and removed 4 (17 requested) atoms. Cycle 49: After refmac, R = 0.2100 (Rfree = 0.000) for 3913 atoms. Found 0 (35 requested) and removed 10 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:26:57 GMT 2018 Job finished. TimeTaking 63.88 Used memory is bytes: 17717832