null Sun 23 Dec 23:49:31 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2h1q-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2h1q-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-mrncs ############### 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 23:49:35 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/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2h1q-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 4816 atoms. Observations/parameters ratio is 0.54 ------------------------------------------------------ Starting model: R = 0.3330 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2447 (Rfree = 0.000) for 4816 atoms. Found 31 (43 requested) and removed 36 (21 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.12 Search for helices and strands: 0 residues in 0 chains, 4902 seeds are put forward NCS extension: 0 residues added, 4902 seeds are put forward Round 1: 251 peptides, 39 chains. Longest chain 23 peptides. Score 0.438 Round 2: 296 peptides, 40 chains. Longest chain 27 peptides. Score 0.531 Round 3: 315 peptides, 41 chains. Longest chain 26 peptides. Score 0.561 Round 4: 319 peptides, 35 chains. Longest chain 28 peptides. Score 0.622 Round 5: 316 peptides, 40 chains. Longest chain 24 peptides. Score 0.572 Taking the results from Round 4 Chains 36, Residues 284, Estimated correctness of the model 46.9 % 4 chains (38 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8451 restraints for refining 3942 atoms. 7213 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2759 (Rfree = 0.000) for 3942 atoms. Found 34 (35 requested) and removed 38 (17 requested) atoms. Cycle 2: After refmac, R = 0.2444 (Rfree = 0.000) for 3908 atoms. Found 8 (35 requested) and removed 28 (17 requested) atoms. Cycle 3: After refmac, R = 0.2363 (Rfree = 0.000) for 3866 atoms. Found 8 (34 requested) and removed 18 (17 requested) atoms. Cycle 4: After refmac, R = 0.2320 (Rfree = 0.000) for 3842 atoms. Found 9 (34 requested) and removed 19 (17 requested) atoms. Cycle 5: After refmac, R = 0.2297 (Rfree = 0.000) for 3824 atoms. Found 6 (34 requested) and removed 17 (17 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3924 seeds are put forward NCS extension: 25 residues added (13 deleted due to clashes), 3949 seeds are put forward Round 1: 282 peptides, 38 chains. Longest chain 20 peptides. Score 0.520 Round 2: 318 peptides, 37 chains. Longest chain 21 peptides. Score 0.603 Round 3: 314 peptides, 36 chains. Longest chain 22 peptides. Score 0.604 Round 4: 311 peptides, 30 chains. Longest chain 23 peptides. Score 0.650 Round 5: 318 peptides, 34 chains. Longest chain 24 peptides. Score 0.629 Taking the results from Round 4 Chains 35, Residues 281, Estimated correctness of the model 53.8 % 4 chains (40 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8029 restraints for refining 3777 atoms. 6810 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2628 (Rfree = 0.000) for 3777 atoms. Found 28 (33 requested) and removed 34 (16 requested) atoms. Cycle 7: After refmac, R = 0.2385 (Rfree = 0.000) for 3760 atoms. Found 8 (33 requested) and removed 20 (16 requested) atoms. Cycle 8: After refmac, R = 0.2271 (Rfree = 0.000) for 3742 atoms. Found 7 (33 requested) and removed 17 (16 requested) atoms. Cycle 9: After refmac, R = 0.2237 (Rfree = 0.000) for 3726 atoms. Found 10 (33 requested) and removed 22 (16 requested) atoms. Cycle 10: After refmac, R = 0.2201 (Rfree = 0.000) for 3698 atoms. Found 9 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3802 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 3826 seeds are put forward Round 1: 290 peptides, 39 chains. Longest chain 42 peptides. Score 0.528 Round 2: 322 peptides, 40 chains. Longest chain 23 peptides. Score 0.584 Round 3: 330 peptides, 36 chains. Longest chain 45 peptides. Score 0.633 Round 4: 315 peptides, 34 chains. Longest chain 46 peptides. Score 0.623 Round 5: 321 peptides, 36 chains. Longest chain 46 peptides. Score 0.617 Taking the results from Round 3 Chains 38, Residues 294, Estimated correctness of the model 49.7 % 5 chains (83 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 7475 restraints for refining 3804 atoms. 6026 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2507 (Rfree = 0.000) for 3804 atoms. Found 34 (34 requested) and removed 33 (17 requested) atoms. Cycle 12: After refmac, R = 0.2241 (Rfree = 0.000) for 3783 atoms. Found 13 (34 requested) and removed 23 (17 requested) atoms. Cycle 13: After refmac, R = 0.2141 (Rfree = 0.000) for 3762 atoms. Found 6 (33 requested) and removed 19 (16 requested) atoms. Cycle 14: After refmac, R = 0.2154 (Rfree = 0.000) for 3737 atoms. Found 7 (33 requested) and removed 21 (16 requested) atoms. Cycle 15: After refmac, R = 0.2062 (Rfree = 0.000) for 3718 atoms. Found 6 (33 requested) and removed 17 (16 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3827 seeds are put forward NCS extension: 14 residues added (19 deleted due to clashes), 3841 seeds are put forward Round 1: 281 peptides, 37 chains. Longest chain 33 peptides. Score 0.528 Round 2: 297 peptides, 32 chains. Longest chain 28 peptides. Score 0.607 Round 3: 300 peptides, 34 chains. Longest chain 44 peptides. Score 0.595 Round 4: 331 peptides, 34 chains. Longest chain 47 peptides. Score 0.651 Round 5: 306 peptides, 34 chains. Longest chain 25 peptides. Score 0.606 Taking the results from Round 4 Chains 38, Residues 297, Estimated correctness of the model 54.1 % 5 chains (97 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 7324 restraints for refining 3803 atoms. 5802 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2447 (Rfree = 0.000) for 3803 atoms. Found 27 (34 requested) and removed 47 (17 requested) atoms. Cycle 17: After refmac, R = 0.2314 (Rfree = 0.000) for 3776 atoms. Found 14 (33 requested) and removed 23 (16 requested) atoms. Cycle 18: After refmac, R = 0.2278 (Rfree = 0.000) for 3759 atoms. Found 8 (33 requested) and removed 21 (16 requested) atoms. Cycle 19: After refmac, R = 0.2177 (Rfree = 0.000) for 3738 atoms. Found 11 (33 requested) and removed 23 (16 requested) atoms. Cycle 20: After refmac, R = 0.2215 (Rfree = 0.000) for 3719 atoms. Found 15 (33 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.28 3.11 Search for helices and strands: 0 residues in 0 chains, 3841 seeds are put forward NCS extension: 51 residues added (34 deleted due to clashes), 3892 seeds are put forward Round 1: 295 peptides, 40 chains. Longest chain 26 peptides. Score 0.529 Round 2: 332 peptides, 37 chains. Longest chain 33 peptides. Score 0.629 Round 3: 337 peptides, 33 chains. Longest chain 35 peptides. Score 0.669 Round 4: 335 peptides, 34 chains. Longest chain 39 peptides. Score 0.658 Round 5: 345 peptides, 30 chains. Longest chain 30 peptides. Score 0.704 Taking the results from Round 5 Chains 32, Residues 315, Estimated correctness of the model 66.0 % 4 chains (57 residues) have been docked in sequence Building loops using Loopy2018 32 chains (315 residues) following loop building 4 chains (57 residues) in sequence following loop building ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 7769 restraints for refining 3875 atoms. 6321 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2469 (Rfree = 0.000) for 3875 atoms. Found 30 (34 requested) and removed 45 (17 requested) atoms. Cycle 22: After refmac, R = 0.2336 (Rfree = 0.000) for 3852 atoms. Found 17 (33 requested) and removed 32 (17 requested) atoms. Cycle 23: After refmac, R = 0.2210 (Rfree = 0.000) for 3823 atoms. Found 11 (33 requested) and removed 31 (17 requested) atoms. Cycle 24: After refmac, R = 0.2189 (Rfree = 0.000) for 3795 atoms. Found 7 (32 requested) and removed 22 (17 requested) atoms. Cycle 25: After refmac, R = 0.2196 (Rfree = 0.000) for 3771 atoms. Found 16 (30 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3883 seeds are put forward NCS extension: 12 residues added (7 deleted due to clashes), 3895 seeds are put forward Round 1: 278 peptides, 38 chains. Longest chain 17 peptides. Score 0.511 Round 2: 295 peptides, 36 chains. Longest chain 19 peptides. Score 0.567 Round 3: 310 peptides, 37 chains. Longest chain 27 peptides. Score 0.588 Round 4: 307 peptides, 36 chains. Longest chain 23 peptides. Score 0.591 Round 5: 316 peptides, 35 chains. Longest chain 24 peptides. Score 0.616 Taking the results from Round 5 Chains 38, Residues 281, Estimated correctness of the model 45.3 % 3 chains (39 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8500 restraints for refining 3943 atoms. 7244 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2292 (Rfree = 0.000) for 3943 atoms. Found 28 (31 requested) and removed 33 (17 requested) atoms. Cycle 27: After refmac, R = 0.2128 (Rfree = 0.000) for 3933 atoms. Found 11 (31 requested) and removed 19 (17 requested) atoms. Cycle 28: After refmac, R = 0.2101 (Rfree = 0.000) for 3918 atoms. Found 11 (31 requested) and removed 21 (17 requested) atoms. Cycle 29: After refmac, R = 0.2091 (Rfree = 0.000) for 3905 atoms. Found 7 (31 requested) and removed 18 (17 requested) atoms. Cycle 30: After refmac, R = 0.2055 (Rfree = 0.000) for 3892 atoms. Found 3 (31 requested) and removed 18 (17 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.31 3.14 Search for helices and strands: 0 residues in 0 chains, 3968 seeds are put forward NCS extension: 23 residues added (6 deleted due to clashes), 3991 seeds are put forward Round 1: 276 peptides, 41 chains. Longest chain 21 peptides. Score 0.476 Round 2: 301 peptides, 39 chains. Longest chain 22 peptides. Score 0.551 Round 3: 308 peptides, 40 chains. Longest chain 20 peptides. Score 0.556 Round 4: 316 peptides, 40 chains. Longest chain 23 peptides. Score 0.572 Round 5: 301 peptides, 36 chains. Longest chain 21 peptides. Score 0.579 Taking the results from Round 5 Chains 37, Residues 265, Estimated correctness of the model 35.3 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8681 restraints for refining 3944 atoms. 7546 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2337 (Rfree = 0.000) for 3944 atoms. Found 27 (31 requested) and removed 31 (17 requested) atoms. Cycle 32: After refmac, R = 0.2299 (Rfree = 0.000) for 3940 atoms. Found 19 (31 requested) and removed 22 (17 requested) atoms. Cycle 33: After refmac, R = 0.2191 (Rfree = 0.000) for 3934 atoms. Found 13 (31 requested) and removed 19 (17 requested) atoms. Cycle 34: After refmac, R = 0.2049 (Rfree = 0.000) for 3920 atoms. Found 4 (31 requested) and removed 21 (17 requested) atoms. Cycle 35: After refmac, R = 0.2061 (Rfree = 0.000) for 3893 atoms. Found 11 (31 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, 4017 seeds are put forward NCS extension: 17 residues added (3 deleted due to clashes), 4034 seeds are put forward Round 1: 281 peptides, 42 chains. Longest chain 18 peptides. Score 0.478 Round 2: 300 peptides, 39 chains. Longest chain 22 peptides. Score 0.549 Round 3: 308 peptides, 35 chains. Longest chain 22 peptides. Score 0.601 Round 4: 289 peptides, 36 chains. Longest chain 22 peptides. Score 0.554 Round 5: 297 peptides, 34 chains. Longest chain 24 peptides. Score 0.589 Taking the results from Round 3 Chains 39, Residues 273, Estimated correctness of the model 41.3 % 4 chains (57 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 8118 restraints for refining 3944 atoms. 6808 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2282 (Rfree = 0.000) for 3944 atoms. Found 30 (31 requested) and removed 31 (17 requested) atoms. Cycle 37: After refmac, R = 0.2083 (Rfree = 0.000) for 3934 atoms. Found 7 (31 requested) and removed 18 (17 requested) atoms. Cycle 38: After refmac, R = 0.2161 (Rfree = 0.000) for 3912 atoms. Found 18 (31 requested) and removed 19 (17 requested) atoms. Cycle 39: After refmac, R = 0.2077 (Rfree = 0.000) for 3900 atoms. Found 19 (31 requested) and removed 20 (17 requested) atoms. Cycle 40: After refmac, R = 0.1916 (Rfree = 0.000) for 3886 atoms. Found 12 (31 requested) and removed 21 (17 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.33 3.16 Search for helices and strands: 0 residues in 0 chains, 3997 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4020 seeds are put forward Round 1: 252 peptides, 43 chains. Longest chain 20 peptides. Score 0.396 Round 2: 281 peptides, 43 chains. Longest chain 22 peptides. Score 0.467 Round 3: 293 peptides, 41 chains. Longest chain 23 peptides. Score 0.515 Round 4: 288 peptides, 43 chains. Longest chain 21 peptides. Score 0.484 Round 5: 284 peptides, 38 chains. Longest chain 21 peptides. Score 0.524 Taking the results from Round 5 Chains 39, Residues 246, Estimated correctness of the model 19.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 10405 reflections ( 99.63 % complete ) and 9143 restraints for refining 3944 atoms. 8179 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2225 (Rfree = 0.000) for 3944 atoms. Found 21 (31 requested) and removed 26 (17 requested) atoms. Cycle 42: After refmac, R = 0.2021 (Rfree = 0.000) for 3932 atoms. Found 14 (31 requested) and removed 22 (17 requested) atoms. Cycle 43: After refmac, R = 0.1958 (Rfree = 0.000) for 3916 atoms. Found 10 (31 requested) and removed 23 (17 requested) atoms. Cycle 44: After refmac, R = 0.1833 (Rfree = 0.000) for 3898 atoms. Found 6 (31 requested) and removed 19 (17 requested) atoms. Cycle 45: After refmac, R = 0.1861 (Rfree = 0.000) for 3881 atoms. Found 15 (31 requested) and removed 19 (17 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.32 3.15 Search for helices and strands: 0 residues in 0 chains, 3990 seeds are put forward NCS extension: 23 residues added (4 deleted due to clashes), 4013 seeds are put forward Round 1: 234 peptides, 40 chains. Longest chain 15 peptides. Score 0.383 Round 2: 261 peptides, 37 chains. Longest chain 20 peptides. Score 0.483 Round 3: 260 peptides, 36 chains. Longest chain 20 peptides. Score 0.491 Round 4: 270 peptides, 35 chains. Longest chain 21 peptides. Score 0.523 Round 5: 268 peptides, 34 chains. Longest chain 17 peptides. Score 0.529 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 234, Estimated correctness of the model 20.5 % 2 chains (16 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (234 residues) following loop building 2 chains (16 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 10405 reflections ( 99.63 % complete ) and 8792 restraints for refining 3944 atoms. 7837 conditional restraints added. Observations/parameters ratio is 0.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2332 (Rfree = 0.000) for 3944 atoms. Found 0 (31 requested) and removed 17 (17 requested) atoms. Cycle 47: After refmac, R = 0.2325 (Rfree = 0.000) for 3919 atoms. Found 0 (31 requested) and removed 17 (17 requested) atoms. Cycle 48: After refmac, R = 0.2433 (Rfree = 0.000) for 3891 atoms. Found 0 (31 requested) and removed 17 (17 requested) atoms. Cycle 49: After refmac, R = 0.2011 (Rfree = 0.000) for 3856 atoms. Found 0 (31 requested) and removed 17 (17 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:39:38 GMT 2018 Job finished. TimeTaking 50.13 Used memory is bytes: 8647080