Sun 23 Dec 23:46:36 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 2hr2-4.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-4.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hr2-4.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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/2hr2-4.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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 23:46:41 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/2hr2-4.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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 865 and 0 Target number of residues in the AU: 865 Target solvent content: 0.6732 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-4.0-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-4.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.80 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: 88.085 4.000 Wilson plot Bfac: 95.09 12411 reflections ( 97.90 % complete ) and 0 restraints for refining 8424 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3317 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3679 (Rfree = 0.000) for 8424 atoms. Found 40 (40 requested) and removed 32 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.89 3.21 Search for helices and strands: 0 residues in 0 chains, 8734 seeds are put forward NCS extension: 0 residues added, 8734 seeds are put forward Round 1: 355 peptides, 61 chains. Longest chain 12 peptides. Score 0.329 Round 2: 433 peptides, 53 chains. Longest chain 18 peptides. Score 0.465 Round 3: 475 peptides, 49 chains. Longest chain 21 peptides. Score 0.529 Round 4: 475 peptides, 48 chains. Longest chain 42 peptides. Score 0.533 Round 5: 490 peptides, 41 chains. Longest chain 39 peptides. Score 0.580 Taking the results from Round 5 Chains 43, Residues 449, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 14652 restraints for refining 6523 atoms. 12852 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2511 (Rfree = 0.000) for 6523 atoms. Found 31 (31 requested) and removed 38 (15 requested) atoms. Cycle 2: After refmac, R = 0.2360 (Rfree = 0.000) for 6386 atoms. Found 30 (30 requested) and removed 29 (15 requested) atoms. Cycle 3: After refmac, R = 0.2321 (Rfree = 0.000) for 6332 atoms. Found 23 (30 requested) and removed 39 (15 requested) atoms. Cycle 4: After refmac, R = 0.2260 (Rfree = 0.000) for 6297 atoms. Found 24 (30 requested) and removed 28 (15 requested) atoms. Cycle 5: After refmac, R = 0.2168 (Rfree = 0.000) for 6275 atoms. Found 10 (29 requested) and removed 43 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 3.16 Search for helices and strands: 0 residues in 0 chains, 6694 seeds are put forward NCS extension: 52 residues added (0 deleted due to clashes), 6746 seeds are put forward Round 1: 449 peptides, 57 chains. Longest chain 23 peptides. Score 0.462 Round 2: 467 peptides, 49 chains. Longest chain 23 peptides. Score 0.521 Round 3: 475 peptides, 47 chains. Longest chain 23 peptides. Score 0.538 Round 4: 477 peptides, 41 chains. Longest chain 32 peptides. Score 0.568 Round 5: 479 peptides, 47 chains. Longest chain 26 peptides. Score 0.542 Taking the results from Round 4 Chains 54, Residues 436, Estimated correctness of the model 0.0 % 11 chains (104 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 12411 reflections ( 97.90 % complete ) and 14407 restraints for refining 6883 atoms. 12377 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2581 (Rfree = 0.000) for 6883 atoms. Found 32 (32 requested) and removed 59 (16 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2515 (Rfree = 0.000) for 6762 atoms. Found 32 (32 requested) and removed 59 (16 requested) atoms. Cycle 8: After refmac, R = 0.2302 (Rfree = 0.000) for 6667 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 9: After refmac, R = 0.2205 (Rfree = 0.000) for 6616 atoms. Found 25 (31 requested) and removed 35 (15 requested) atoms. Cycle 10: After refmac, R = 0.2164 (Rfree = 0.000) for 6573 atoms. Found 19 (31 requested) and removed 36 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.83 3.16 Search for helices and strands: 0 residues in 0 chains, 6978 seeds are put forward NCS extension: 47 residues added (3 deleted due to clashes), 7025 seeds are put forward Round 1: 473 peptides, 67 chains. Longest chain 17 peptides. Score 0.438 Round 2: 492 peptides, 52 chains. Longest chain 22 peptides. Score 0.531 Round 3: 482 peptides, 54 chains. Longest chain 31 peptides. Score 0.512 Round 4: 476 peptides, 49 chains. Longest chain 43 peptides. Score 0.530 Round 5: 497 peptides, 52 chains. Longest chain 31 peptides. Score 0.536 Taking the results from Round 5 Chains 55, Residues 445, Estimated correctness of the model 0.0 % 4 chains (30 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15251 restraints for refining 6890 atoms. 13415 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2463 (Rfree = 0.000) for 6890 atoms. Found 32 (32 requested) and removed 47 (16 requested) atoms. Cycle 12: After refmac, R = 0.2174 (Rfree = 0.000) for 6798 atoms. Found 28 (32 requested) and removed 37 (16 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1936 (Rfree = 0.000) for 6759 atoms. Found 11 (32 requested) and removed 29 (16 requested) atoms. Cycle 14: After refmac, R = 0.1926 (Rfree = 0.000) for 6723 atoms. Found 9 (32 requested) and removed 34 (16 requested) atoms. Cycle 15: After refmac, R = 0.1860 (Rfree = 0.000) for 6685 atoms. Found 4 (31 requested) and removed 20 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.85 3.18 Search for helices and strands: 0 residues in 0 chains, 7123 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 7149 seeds are put forward Round 1: 459 peptides, 69 chains. Longest chain 15 peptides. Score 0.412 Round 2: 502 peptides, 61 chains. Longest chain 20 peptides. Score 0.498 Round 3: 500 peptides, 58 chains. Longest chain 27 peptides. Score 0.511 Round 4: 492 peptides, 59 chains. Longest chain 23 peptides. Score 0.498 Round 5: 484 peptides, 56 chains. Longest chain 21 peptides. Score 0.504 Taking the results from Round 3 Chains 62, Residues 442, Estimated correctness of the model 0.0 % 4 chains (41 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15062 restraints for refining 6892 atoms. 13194 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2469 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 48 (16 requested) atoms. Cycle 17: After refmac, R = 0.2395 (Rfree = 0.000) for 6819 atoms. Found 32 (32 requested) and removed 45 (16 requested) atoms. Cycle 18: After refmac, R = 0.2279 (Rfree = 0.000) for 6777 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 19: After refmac, R = 0.2157 (Rfree = 0.000) for 6749 atoms. Found 27 (32 requested) and removed 33 (16 requested) atoms. Cycle 20: After refmac, R = 0.1928 (Rfree = 0.000) for 6731 atoms. Found 9 (32 requested) and removed 24 (16 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 3.17 Search for helices and strands: 0 residues in 0 chains, 7125 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7144 seeds are put forward Round 1: 449 peptides, 72 chains. Longest chain 18 peptides. Score 0.385 Round 2: 467 peptides, 57 chains. Longest chain 19 peptides. Score 0.481 Round 3: 482 peptides, 55 chains. Longest chain 24 peptides. Score 0.507 Round 4: 472 peptides, 54 chains. Longest chain 24 peptides. Score 0.501 Round 5: 487 peptides, 51 chains. Longest chain 29 peptides. Score 0.531 Taking the results from Round 5 Chains 51, Residues 436, Estimated correctness of the model 0.0 % 2 chains (12 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15283 restraints for refining 6891 atoms. 13549 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2615 (Rfree = 0.000) for 6891 atoms. Found 32 (32 requested) and removed 69 (16 requested) atoms. Cycle 22: After refmac, R = 0.2332 (Rfree = 0.000) for 6787 atoms. Found 32 (32 requested) and removed 64 (16 requested) atoms. Cycle 23: After refmac, R = 0.2026 (Rfree = 0.000) for 6726 atoms. Found 11 (32 requested) and removed 45 (16 requested) atoms. Cycle 24: After refmac, R = 0.2133 (Rfree = 0.000) for 6673 atoms. Found 17 (31 requested) and removed 24 (15 requested) atoms. Cycle 25: After refmac, R = 0.2114 (Rfree = 0.000) for 6656 atoms. Found 20 (31 requested) and removed 26 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.84 3.17 Search for helices and strands: 0 residues in 0 chains, 7049 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 7069 seeds are put forward Round 1: 423 peptides, 70 chains. Longest chain 14 peptides. Score 0.364 Round 2: 462 peptides, 63 chains. Longest chain 19 peptides. Score 0.446 Round 3: 465 peptides, 55 chains. Longest chain 30 peptides. Score 0.489 Round 4: 479 peptides, 56 chains. Longest chain 23 peptides. Score 0.499 Round 5: 471 peptides, 57 chains. Longest chain 22 peptides. Score 0.486 Taking the results from Round 4 Chains 56, Residues 423, Estimated correctness of the model 0.0 % 1 chains (15 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15392 restraints for refining 6893 atoms. 13693 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2401 (Rfree = 0.000) for 6893 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 27: After refmac, R = 0.2234 (Rfree = 0.000) for 6827 atoms. Found 27 (32 requested) and removed 33 (16 requested) atoms. Cycle 28: After refmac, R = 0.2213 (Rfree = 0.000) for 6785 atoms. Found 32 (32 requested) and removed 55 (16 requested) atoms. Cycle 29: After refmac, R = 0.2131 (Rfree = 0.000) for 6723 atoms. Found 32 (32 requested) and removed 56 (16 requested) atoms. Cycle 30: After refmac, R = 0.1826 (Rfree = 0.000) for 6672 atoms. Found 10 (31 requested) and removed 28 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.82 3.15 Search for helices and strands: 0 residues in 0 chains, 7028 seeds are put forward NCS extension: 39 residues added (4 deleted due to clashes), 7067 seeds are put forward Round 1: 409 peptides, 69 chains. Longest chain 15 peptides. Score 0.352 Round 2: 461 peptides, 68 chains. Longest chain 15 peptides. Score 0.419 Round 3: 483 peptides, 63 chains. Longest chain 16 peptides. Score 0.469 Round 4: 478 peptides, 62 chains. Longest chain 18 peptides. Score 0.468 Round 5: 487 peptides, 59 chains. Longest chain 27 peptides. Score 0.493 Taking the results from Round 5 Chains 62, Residues 428, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15342 restraints for refining 6892 atoms. 13616 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2380 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 32: After refmac, R = 0.2092 (Rfree = 0.000) for 6838 atoms. Found 23 (32 requested) and removed 30 (16 requested) atoms. Cycle 33: After refmac, R = 0.2044 (Rfree = 0.000) for 6808 atoms. Found 21 (32 requested) and removed 27 (16 requested) atoms. Cycle 34: After refmac, R = 0.1995 (Rfree = 0.000) for 6791 atoms. Found 22 (32 requested) and removed 30 (16 requested) atoms. Cycle 35: After refmac, R = 0.1921 (Rfree = 0.000) for 6769 atoms. Found 18 (32 requested) and removed 29 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.83 3.16 Search for helices and strands: 0 residues in 0 chains, 7080 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 7099 seeds are put forward Round 1: 418 peptides, 72 chains. Longest chain 14 peptides. Score 0.347 Round 2: 448 peptides, 63 chains. Longest chain 18 peptides. Score 0.430 Round 3: 451 peptides, 62 chains. Longest chain 19 peptides. Score 0.439 Round 4: 454 peptides, 63 chains. Longest chain 15 peptides. Score 0.437 Round 5: 445 peptides, 54 chains. Longest chain 20 peptides. Score 0.473 Taking the results from Round 5 Chains 56, Residues 391, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15882 restraints for refining 6892 atoms. 14312 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2566 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 37: After refmac, R = 0.2166 (Rfree = 0.000) for 6844 atoms. Found 30 (32 requested) and removed 26 (16 requested) atoms. Cycle 38: After refmac, R = 0.2183 (Rfree = 0.000) for 6836 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 39: After refmac, R = 0.2085 (Rfree = 0.000) for 6822 atoms. Found 28 (32 requested) and removed 22 (16 requested) atoms. Cycle 40: After refmac, R = 0.2069 (Rfree = 0.000) for 6813 atoms. Found 29 (32 requested) and removed 36 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 3.15 Search for helices and strands: 0 residues in 0 chains, 7166 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 7179 seeds are put forward Round 1: 362 peptides, 66 chains. Longest chain 15 peptides. Score 0.309 Round 2: 422 peptides, 60 chains. Longest chain 16 peptides. Score 0.416 Round 3: 409 peptides, 64 chains. Longest chain 15 peptides. Score 0.380 Round 4: 427 peptides, 63 chains. Longest chain 15 peptides. Score 0.406 Round 5: 440 peptides, 66 chains. Longest chain 15 peptides. Score 0.406 Taking the results from Round 2 Chains 60, Residues 362, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 16154 restraints for refining 6893 atoms. 14766 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2272 (Rfree = 0.000) for 6893 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 42: After refmac, R = 0.2199 (Rfree = 0.000) for 6859 atoms. Found 32 (32 requested) and removed 50 (16 requested) atoms. Cycle 43: After refmac, R = 0.2206 (Rfree = 0.000) for 6825 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 44: After refmac, R = 0.2160 (Rfree = 0.000) for 6800 atoms. Found 32 (32 requested) and removed 38 (16 requested) atoms. Cycle 45: After refmac, R = 0.2156 (Rfree = 0.000) for 6778 atoms. Found 32 (32 requested) and removed 39 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.81 3.15 Search for helices and strands: 0 residues in 0 chains, 7130 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 7143 seeds are put forward Round 1: 361 peptides, 74 chains. Longest chain 11 peptides. Score 0.262 Round 2: 426 peptides, 70 chains. Longest chain 12 peptides. Score 0.368 Round 3: 427 peptides, 71 chains. Longest chain 15 peptides. Score 0.363 Round 4: 428 peptides, 66 chains. Longest chain 16 peptides. Score 0.391 Round 5: 417 peptides, 63 chains. Longest chain 20 peptides. Score 0.394 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 63, Residues 354, 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 2hr2-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12411 reflections ( 97.90 % complete ) and 16104 restraints for refining 6893 atoms. 14751 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2318 (Rfree = 0.000) for 6893 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2164 (Rfree = 0.000) for 6835 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2249 (Rfree = 0.000) for 6793 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2273 (Rfree = 0.000) for 6747 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Writing output files ... TimeTaking 81