Sun 23 Dec 22:22:49 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 2hi0-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hi0-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.2-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/2hi0-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.2-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 22:22:59 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/2hi0-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hi0-3.2-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 334 and 0 Target number of residues in the AU: 334 Target solvent content: 0.6116 Checking the provided sequence file Detected sequence length: 240 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 480 Adjusted target solvent content: 0.44 Input MTZ file: 2hi0-3.2-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: 4 Cell parameters: 58.636 38.695 103.583 90.000 98.094 90.000 Input sequence file: 2hi0-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 3840 target number of atoms Had to go as low as 0.65 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: 102.551 3.200 Wilson plot Bfac: 57.25 7883 reflections ( 99.82 % complete ) and 0 restraints for refining 4274 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3156 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2651 (Rfree = 0.000) for 4274 atoms. Found 38 (38 requested) and removed 49 (19 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 3.37 Search for helices and strands: 0 residues in 0 chains, 4373 seeds are put forward NCS extension: 0 residues added, 4373 seeds are put forward Round 1: 204 peptides, 43 chains. Longest chain 8 peptides. Score 0.291 Round 2: 271 peptides, 48 chains. Longest chain 19 peptides. Score 0.448 Round 3: 285 peptides, 40 chains. Longest chain 18 peptides. Score 0.587 Round 4: 296 peptides, 37 chains. Longest chain 21 peptides. Score 0.646 Round 5: 300 peptides, 34 chains. Longest chain 30 peptides. Score 0.684 Taking the results from Round 5 Chains 35, Residues 266, Estimated correctness of the model 61.7 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7519 restraints for refining 3506 atoms. 6452 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2537 (Rfree = 0.000) for 3506 atoms. Found 28 (31 requested) and removed 24 (15 requested) atoms. Cycle 2: After refmac, R = 0.2467 (Rfree = 0.000) for 3478 atoms. Found 17 (31 requested) and removed 21 (15 requested) atoms. Cycle 3: After refmac, R = 0.2372 (Rfree = 0.000) for 3459 atoms. Found 11 (31 requested) and removed 18 (15 requested) atoms. Cycle 4: After refmac, R = 0.2309 (Rfree = 0.000) for 3444 atoms. Found 9 (30 requested) and removed 19 (15 requested) atoms. Cycle 5: After refmac, R = 0.2126 (Rfree = 0.000) for 3427 atoms. Found 11 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 3547 seeds are put forward NCS extension: 20 residues added (6 deleted due to clashes), 3567 seeds are put forward Round 1: 234 peptides, 40 chains. Longest chain 14 peptides. Score 0.439 Round 2: 284 peptides, 35 chains. Longest chain 32 peptides. Score 0.639 Round 3: 288 peptides, 37 chains. Longest chain 18 peptides. Score 0.627 Round 4: 308 peptides, 39 chains. Longest chain 27 peptides. Score 0.653 Round 5: 298 peptides, 36 chains. Longest chain 22 peptides. Score 0.660 Taking the results from Round 5 Chains 39, Residues 262, Estimated correctness of the model 56.2 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7543 restraints for refining 3504 atoms. 6447 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2386 (Rfree = 0.000) for 3504 atoms. Found 25 (31 requested) and removed 30 (15 requested) atoms. Cycle 7: After refmac, R = 0.2278 (Rfree = 0.000) for 3476 atoms. Found 27 (31 requested) and removed 20 (15 requested) atoms. Cycle 8: After refmac, R = 0.2179 (Rfree = 0.000) for 3468 atoms. Found 18 (31 requested) and removed 21 (15 requested) atoms. Cycle 9: After refmac, R = 0.2120 (Rfree = 0.000) for 3461 atoms. Found 11 (31 requested) and removed 18 (15 requested) atoms. Cycle 10: After refmac, R = 0.2092 (Rfree = 0.000) for 3445 atoms. Found 16 (30 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.34 Search for helices and strands: 0 residues in 0 chains, 3590 seeds are put forward NCS extension: 34 residues added (2 deleted due to clashes), 3624 seeds are put forward Round 1: 250 peptides, 40 chains. Longest chain 15 peptides. Score 0.489 Round 2: 274 peptides, 41 chains. Longest chain 20 peptides. Score 0.546 Round 3: 281 peptides, 37 chains. Longest chain 22 peptides. Score 0.610 Round 4: 291 peptides, 40 chains. Longest chain 28 peptides. Score 0.602 Round 5: 285 peptides, 39 chains. Longest chain 16 peptides. Score 0.598 Taking the results from Round 3 Chains 37, Residues 244, Estimated correctness of the model 43.7 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7864 restraints for refining 3506 atoms. 6917 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2154 (Rfree = 0.000) for 3506 atoms. Found 23 (31 requested) and removed 17 (15 requested) atoms. Cycle 12: After refmac, R = 0.2052 (Rfree = 0.000) for 3509 atoms. Found 13 (31 requested) and removed 15 (15 requested) atoms. Cycle 13: After refmac, R = 0.1989 (Rfree = 0.000) for 3500 atoms. Found 11 (31 requested) and removed 15 (15 requested) atoms. Cycle 14: After refmac, R = 0.1953 (Rfree = 0.000) for 3492 atoms. Found 15 (31 requested) and removed 15 (15 requested) atoms. Cycle 15: After refmac, R = 0.1919 (Rfree = 0.000) for 3489 atoms. Found 6 (31 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 3613 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3639 seeds are put forward Round 1: 237 peptides, 40 chains. Longest chain 13 peptides. Score 0.448 Round 2: 274 peptides, 39 chains. Longest chain 19 peptides. Score 0.570 Round 3: 280 peptides, 38 chains. Longest chain 23 peptides. Score 0.597 Round 4: 289 peptides, 40 chains. Longest chain 23 peptides. Score 0.597 Round 5: 277 peptides, 36 chains. Longest chain 23 peptides. Score 0.612 Taking the results from Round 5 Chains 36, Residues 241, Estimated correctness of the model 44.3 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7759 restraints for refining 3506 atoms. 6826 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2065 (Rfree = 0.000) for 3506 atoms. Found 26 (31 requested) and removed 17 (15 requested) atoms. Cycle 17: After refmac, R = 0.1945 (Rfree = 0.000) for 3510 atoms. Found 10 (31 requested) and removed 16 (15 requested) atoms. Cycle 18: After refmac, R = 0.1906 (Rfree = 0.000) for 3500 atoms. Found 15 (31 requested) and removed 15 (15 requested) atoms. Cycle 19: After refmac, R = 0.1848 (Rfree = 0.000) for 3495 atoms. Found 12 (31 requested) and removed 15 (15 requested) atoms. Cycle 20: After refmac, R = 0.1796 (Rfree = 0.000) for 3484 atoms. Found 12 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.07 3.33 Search for helices and strands: 0 residues in 0 chains, 3605 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 3628 seeds are put forward Round 1: 221 peptides, 40 chains. Longest chain 10 peptides. Score 0.396 Round 2: 258 peptides, 37 chains. Longest chain 23 peptides. Score 0.550 Round 3: 259 peptides, 36 chains. Longest chain 23 peptides. Score 0.565 Round 4: 268 peptides, 36 chains. Longest chain 18 peptides. Score 0.589 Round 5: 257 peptides, 34 chains. Longest chain 23 peptides. Score 0.583 Taking the results from Round 4 Chains 39, Residues 232, Estimated correctness of the model 38.1 % 5 chains (38 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7508 restraints for refining 3506 atoms. 6484 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2023 (Rfree = 0.000) for 3506 atoms. Found 28 (31 requested) and removed 21 (15 requested) atoms. Cycle 22: After refmac, R = 0.1870 (Rfree = 0.000) for 3506 atoms. Found 10 (31 requested) and removed 17 (15 requested) atoms. Cycle 23: After refmac, R = 0.1848 (Rfree = 0.000) for 3491 atoms. Found 13 (31 requested) and removed 16 (15 requested) atoms. Cycle 24: After refmac, R = 0.1741 (Rfree = 0.000) for 3485 atoms. Found 14 (31 requested) and removed 15 (15 requested) atoms. Cycle 25: After refmac, R = 0.1655 (Rfree = 0.000) for 3482 atoms. Found 10 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.35 Search for helices and strands: 0 residues in 0 chains, 3608 seeds are put forward NCS extension: 31 residues added (1 deleted due to clashes), 3639 seeds are put forward Round 1: 221 peptides, 42 chains. Longest chain 9 peptides. Score 0.367 Round 2: 235 peptides, 39 chains. Longest chain 16 peptides. Score 0.456 Round 3: 244 peptides, 36 chains. Longest chain 21 peptides. Score 0.523 Round 4: 238 peptides, 38 chains. Longest chain 14 peptides. Score 0.479 Round 5: 240 peptides, 38 chains. Longest chain 18 peptides. Score 0.485 Taking the results from Round 3 Chains 36, Residues 208, Estimated correctness of the model 18.7 % 2 chains (23 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7717 restraints for refining 3506 atoms. 6846 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1917 (Rfree = 0.000) for 3506 atoms. Found 27 (31 requested) and removed 22 (15 requested) atoms. Cycle 27: After refmac, R = 0.1799 (Rfree = 0.000) for 3507 atoms. Found 15 (31 requested) and removed 15 (15 requested) atoms. Cycle 28: After refmac, R = 0.1740 (Rfree = 0.000) for 3505 atoms. Found 11 (31 requested) and removed 15 (15 requested) atoms. Cycle 29: After refmac, R = 0.1709 (Rfree = 0.000) for 3498 atoms. Found 9 (31 requested) and removed 15 (15 requested) atoms. Cycle 30: After refmac, R = 0.1656 (Rfree = 0.000) for 3490 atoms. Found 5 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.10 3.36 Search for helices and strands: 0 residues in 0 chains, 3610 seeds are put forward NCS extension: 0 residues added, 3610 seeds are put forward Round 1: 209 peptides, 39 chains. Longest chain 16 peptides. Score 0.369 Round 2: 237 peptides, 40 chains. Longest chain 15 peptides. Score 0.448 Round 3: 228 peptides, 36 chains. Longest chain 20 peptides. Score 0.474 Round 4: 224 peptides, 33 chains. Longest chain 23 peptides. Score 0.503 Round 5: 232 peptides, 35 chains. Longest chain 17 peptides. Score 0.500 Taking the results from Round 4 Chains 34, Residues 191, Estimated correctness of the model 12.3 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7812 restraints for refining 3506 atoms. 7023 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1914 (Rfree = 0.000) for 3506 atoms. Found 22 (31 requested) and removed 19 (15 requested) atoms. Cycle 32: After refmac, R = 0.1834 (Rfree = 0.000) for 3506 atoms. Found 14 (31 requested) and removed 16 (15 requested) atoms. Cycle 33: After refmac, R = 0.1992 (Rfree = 0.000) for 3503 atoms. Found 19 (31 requested) and removed 16 (15 requested) atoms. Cycle 34: After refmac, R = 0.2093 (Rfree = 0.000) for 3501 atoms. Found 28 (31 requested) and removed 15 (15 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1964 (Rfree = 0.000) for 3511 atoms. Found 23 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 3639 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3665 seeds are put forward Round 1: 199 peptides, 33 chains. Longest chain 21 peptides. Score 0.423 Round 2: 229 peptides, 33 chains. Longest chain 29 peptides. Score 0.517 Round 3: 234 peptides, 32 chains. Longest chain 24 peptides. Score 0.545 Round 4: 236 peptides, 31 chains. Longest chain 18 peptides. Score 0.563 Round 5: 226 peptides, 28 chains. Longest chain 27 peptides. Score 0.573 Taking the results from Round 5 Chains 29, Residues 198, Estimated correctness of the model 33.6 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7843 restraints for refining 3505 atoms. 7013 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1930 (Rfree = 0.000) for 3505 atoms. Found 22 (31 requested) and removed 16 (15 requested) atoms. Cycle 37: After refmac, R = 0.1857 (Rfree = 0.000) for 3508 atoms. Found 10 (31 requested) and removed 15 (15 requested) atoms. Cycle 38: After refmac, R = 0.1767 (Rfree = 0.000) for 3501 atoms. Found 6 (31 requested) and removed 15 (15 requested) atoms. Cycle 39: After refmac, R = 0.2056 (Rfree = 0.000) for 3490 atoms. Found 27 (31 requested) and removed 15 (15 requested) atoms. Cycle 40: After refmac, R = 0.1632 (Rfree = 0.000) for 3498 atoms. Found 5 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.06 3.32 Search for helices and strands: 0 residues in 0 chains, 3595 seeds are put forward NCS extension: 42 residues added (2 deleted due to clashes), 3637 seeds are put forward Round 1: 196 peptides, 33 chains. Longest chain 17 peptides. Score 0.413 Round 2: 213 peptides, 32 chains. Longest chain 17 peptides. Score 0.482 Round 3: 225 peptides, 33 chains. Longest chain 25 peptides. Score 0.506 Round 4: 217 peptides, 34 chains. Longest chain 17 peptides. Score 0.467 Round 5: 226 peptides, 32 chains. Longest chain 26 peptides. Score 0.522 Taking the results from Round 5 Chains 34, Residues 194, Estimated correctness of the model 18.3 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 7883 reflections ( 99.82 % complete ) and 7689 restraints for refining 3506 atoms. 6842 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1882 (Rfree = 0.000) for 3506 atoms. Found 19 (31 requested) and removed 15 (15 requested) atoms. Cycle 42: After refmac, R = 0.1754 (Rfree = 0.000) for 3508 atoms. Found 10 (31 requested) and removed 15 (15 requested) atoms. Cycle 43: After refmac, R = 0.1620 (Rfree = 0.000) for 3498 atoms. Found 9 (31 requested) and removed 17 (15 requested) atoms. Cycle 44: After refmac, R = 0.1616 (Rfree = 0.000) for 3489 atoms. Found 13 (31 requested) and removed 16 (15 requested) atoms. Cycle 45: After refmac, R = 0.1661 (Rfree = 0.000) for 3482 atoms. Found 9 (31 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.28 Search for helices and strands: 0 residues in 0 chains, 3566 seeds are put forward NCS extension: 30 residues added (0 deleted due to clashes), 3596 seeds are put forward Round 1: 191 peptides, 36 chains. Longest chain 11 peptides. Score 0.350 Round 2: 212 peptides, 32 chains. Longest chain 26 peptides. Score 0.479 Round 3: 211 peptides, 30 chains. Longest chain 20 peptides. Score 0.503 Round 4: 215 peptides, 35 chains. Longest chain 19 peptides. Score 0.447 Round 5: 221 peptides, 32 chains. Longest chain 23 peptides. Score 0.507 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 34, Residues 189, Estimated correctness of the model 13.6 % 2 chains (32 residues) have been docked in sequence Sequence coverage is 16 % Consider running further cycles of model building using 2hi0-3_warpNtrace.pdb as input Building loops using Loopy2018 34 chains (189 residues) following loop building 2 chains (32 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 7883 reflections ( 99.82 % complete ) and 7606 restraints for refining 3504 atoms. 6764 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1892 (Rfree = 0.000) for 3504 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 3485 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 48: After refmac, R = 0.1973 (Rfree = 0.000) for 3468 atoms. Found 0 (31 requested) and removed 15 (15 requested) atoms. Cycle 49: After refmac, R = 0.1642 (Rfree = 0.000) for 3446 atoms. TimeTaking 55.18