Sun 23 Dec 22:22:46 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 1vkh-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkh-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.4-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/1vkh-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.4-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 22:22:56 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/1vkh-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkh-3.4-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 380 and 0 Target number of residues in the AU: 380 Target solvent content: 0.5918 Checking the provided sequence file Detected sequence length: 273 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 546 Adjusted target solvent content: 0.41 Input MTZ file: 1vkh-3.4-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: 41.965 85.956 70.476 90.000 97.713 90.000 Input sequence file: 1vkh-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 4368 target number of atoms Had to go as low as 0.60 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: 19.289 3.400 Wilson plot Bfac: 49.34 6884 reflections ( 99.41 % complete ) and 0 restraints for refining 4834 atoms. Observations/parameters ratio is 0.36 ------------------------------------------------------ Starting model: R = 0.3198 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2992 (Rfree = 0.000) for 4834 atoms. Found 36 (36 requested) and removed 99 (18 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.96 3.34 Search for helices and strands: 0 residues in 0 chains, 4888 seeds are put forward NCS extension: 0 residues added, 4888 seeds are put forward Round 1: 206 peptides, 42 chains. Longest chain 10 peptides. Score 0.304 Round 2: 256 peptides, 48 chains. Longest chain 11 peptides. Score 0.386 Round 3: 274 peptides, 43 chains. Longest chain 13 peptides. Score 0.502 Round 4: 291 peptides, 43 chains. Longest chain 17 peptides. Score 0.547 Round 5: 269 peptides, 40 chains. Longest chain 16 peptides. Score 0.524 Taking the results from Round 4 Chains 43, Residues 248, Estimated correctness of the model 10.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8987 restraints for refining 3970 atoms. 8038 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2345 (Rfree = 0.000) for 3970 atoms. Found 24 (29 requested) and removed 31 (14 requested) atoms. Cycle 2: After refmac, R = 0.2226 (Rfree = 0.000) for 3934 atoms. Found 29 (29 requested) and removed 30 (14 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2175 (Rfree = 0.000) for 3919 atoms. Found 19 (29 requested) and removed 19 (14 requested) atoms. Cycle 4: After refmac, R = 0.2153 (Rfree = 0.000) for 3911 atoms. Found 24 (29 requested) and removed 18 (14 requested) atoms. Cycle 5: After refmac, R = 0.2073 (Rfree = 0.000) for 3912 atoms. Found 20 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 4075 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 4092 seeds are put forward Round 1: 232 peptides, 47 chains. Longest chain 12 peptides. Score 0.322 Round 2: 267 peptides, 46 chains. Longest chain 15 peptides. Score 0.445 Round 3: 266 peptides, 45 chains. Longest chain 16 peptides. Score 0.455 Round 4: 274 peptides, 42 chains. Longest chain 18 peptides. Score 0.514 Round 5: 276 peptides, 42 chains. Longest chain 16 peptides. Score 0.519 Taking the results from Round 5 Chains 42, Residues 234, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9281 restraints for refining 3971 atoms. 8387 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2218 (Rfree = 0.000) for 3971 atoms. Found 15 (29 requested) and removed 30 (14 requested) atoms. Cycle 7: After refmac, R = 0.2051 (Rfree = 0.000) for 3943 atoms. Found 26 (29 requested) and removed 20 (14 requested) atoms. Cycle 8: After refmac, R = 0.1997 (Rfree = 0.000) for 3942 atoms. Found 19 (29 requested) and removed 24 (14 requested) atoms. Cycle 9: After refmac, R = 0.1949 (Rfree = 0.000) for 3933 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 10: After refmac, R = 0.1845 (Rfree = 0.000) for 3939 atoms. Found 14 (29 requested) and removed 21 (14 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.02 3.41 Search for helices and strands: 0 residues in 0 chains, 4085 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 4099 seeds are put forward Round 1: 232 peptides, 43 chains. Longest chain 16 peptides. Score 0.377 Round 2: 262 peptides, 41 chains. Longest chain 18 peptides. Score 0.492 Round 3: 286 peptides, 43 chains. Longest chain 15 peptides. Score 0.534 Round 4: 291 peptides, 44 chains. Longest chain 15 peptides. Score 0.536 Round 5: 270 peptides, 38 chains. Longest chain 20 peptides. Score 0.549 Taking the results from Round 5 Chains 38, Residues 232, Estimated correctness of the model 11.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9339 restraints for refining 3971 atoms. 8449 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2100 (Rfree = 0.000) for 3971 atoms. Found 23 (29 requested) and removed 19 (14 requested) atoms. Cycle 12: After refmac, R = 0.1903 (Rfree = 0.000) for 3967 atoms. Found 12 (30 requested) and removed 20 (15 requested) atoms. Cycle 13: After refmac, R = 0.1900 (Rfree = 0.000) for 3955 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. Cycle 14: After refmac, R = 0.1882 (Rfree = 0.000) for 3946 atoms. Found 11 (29 requested) and removed 17 (14 requested) atoms. Cycle 15: After refmac, R = 0.1836 (Rfree = 0.000) for 3938 atoms. Found 20 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 4073 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 4096 seeds are put forward Round 1: 219 peptides, 39 chains. Longest chain 15 peptides. Score 0.390 Round 2: 231 peptides, 35 chains. Longest chain 18 peptides. Score 0.479 Round 3: 251 peptides, 34 chains. Longest chain 25 peptides. Score 0.546 Round 4: 245 peptides, 36 chains. Longest chain 17 peptides. Score 0.506 Round 5: 262 peptides, 33 chains. Longest chain 16 peptides. Score 0.585 Taking the results from Round 5 Chains 33, Residues 229, Estimated correctness of the model 23.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9213 restraints for refining 3971 atoms. 8330 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2051 (Rfree = 0.000) for 3971 atoms. Found 28 (29 requested) and removed 20 (14 requested) atoms. Cycle 17: After refmac, R = 0.1836 (Rfree = 0.000) for 3971 atoms. Found 9 (30 requested) and removed 19 (15 requested) atoms. Cycle 18: After refmac, R = 0.1824 (Rfree = 0.000) for 3957 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. Cycle 19: After refmac, R = 0.1850 (Rfree = 0.000) for 3948 atoms. Found 6 (29 requested) and removed 17 (14 requested) atoms. Cycle 20: After refmac, R = 0.1811 (Rfree = 0.000) for 3936 atoms. Found 15 (29 requested) and removed 14 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 4093 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 4110 seeds are put forward Round 1: 216 peptides, 39 chains. Longest chain 15 peptides. Score 0.380 Round 2: 236 peptides, 41 chains. Longest chain 16 peptides. Score 0.416 Round 3: 252 peptides, 38 chains. Longest chain 19 peptides. Score 0.501 Round 4: 256 peptides, 38 chains. Longest chain 17 peptides. Score 0.512 Round 5: 252 peptides, 37 chains. Longest chain 19 peptides. Score 0.513 Taking the results from Round 5 Chains 37, Residues 215, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9287 restraints for refining 3971 atoms. 8464 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2082 (Rfree = 0.000) for 3971 atoms. Found 25 (29 requested) and removed 20 (14 requested) atoms. Cycle 22: After refmac, R = 0.1899 (Rfree = 0.000) for 3968 atoms. Found 12 (30 requested) and removed 18 (15 requested) atoms. Cycle 23: After refmac, R = 0.1886 (Rfree = 0.000) for 3957 atoms. Found 13 (29 requested) and removed 18 (14 requested) atoms. Cycle 24: After refmac, R = 0.1841 (Rfree = 0.000) for 3948 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. Cycle 25: After refmac, R = 0.1863 (Rfree = 0.000) for 3945 atoms. Found 17 (29 requested) and removed 15 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 4119 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 4142 seeds are put forward Round 1: 220 peptides, 41 chains. Longest chain 11 peptides. Score 0.365 Round 2: 261 peptides, 43 chains. Longest chain 14 peptides. Score 0.465 Round 3: 249 peptides, 40 chains. Longest chain 15 peptides. Score 0.468 Round 4: 251 peptides, 39 chains. Longest chain 19 peptides. Score 0.486 Round 5: 266 peptides, 39 chains. Longest chain 19 peptides. Score 0.527 Taking the results from Round 5 Chains 39, Residues 227, Estimated correctness of the model 3.1 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 8971 restraints for refining 3971 atoms. 7998 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2085 (Rfree = 0.000) for 3971 atoms. Found 24 (29 requested) and removed 22 (14 requested) atoms. Cycle 27: After refmac, R = 0.1997 (Rfree = 0.000) for 3963 atoms. Found 14 (29 requested) and removed 17 (14 requested) atoms. Cycle 28: After refmac, R = 0.1928 (Rfree = 0.000) for 3954 atoms. Found 20 (29 requested) and removed 17 (14 requested) atoms. Cycle 29: After refmac, R = 0.1864 (Rfree = 0.000) for 3952 atoms. Found 20 (29 requested) and removed 17 (14 requested) atoms. Cycle 30: After refmac, R = 0.1792 (Rfree = 0.000) for 3950 atoms. Found 20 (29 requested) and removed 17 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.03 3.42 Search for helices and strands: 0 residues in 0 chains, 4074 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 4103 seeds are put forward Round 1: 210 peptides, 42 chains. Longest chain 10 peptides. Score 0.318 Round 2: 249 peptides, 40 chains. Longest chain 14 peptides. Score 0.468 Round 3: 242 peptides, 40 chains. Longest chain 10 peptides. Score 0.447 Round 4: 232 peptides, 33 chains. Longest chain 16 peptides. Score 0.507 Round 5: 250 peptides, 41 chains. Longest chain 12 peptides. Score 0.458 Taking the results from Round 4 Chains 33, Residues 199, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9302 restraints for refining 3971 atoms. 8539 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2001 (Rfree = 0.000) for 3971 atoms. Found 25 (29 requested) and removed 22 (14 requested) atoms. Cycle 32: After refmac, R = 0.1798 (Rfree = 0.000) for 3969 atoms. Found 16 (30 requested) and removed 19 (15 requested) atoms. Cycle 33: After refmac, R = 0.1790 (Rfree = 0.000) for 3963 atoms. Found 15 (29 requested) and removed 14 (14 requested) atoms. Cycle 34: After refmac, R = 0.1726 (Rfree = 0.000) for 3962 atoms. Found 13 (29 requested) and removed 18 (14 requested) atoms. Cycle 35: After refmac, R = 0.1725 (Rfree = 0.000) for 3954 atoms. Found 16 (29 requested) and removed 16 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 4073 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 4096 seeds are put forward Round 1: 203 peptides, 42 chains. Longest chain 9 peptides. Score 0.294 Round 2: 226 peptides, 36 chains. Longest chain 14 peptides. Score 0.451 Round 3: 244 peptides, 40 chains. Longest chain 13 peptides. Score 0.453 Round 4: 232 peptides, 38 chains. Longest chain 14 peptides. Score 0.443 Round 5: 238 peptides, 40 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 3 Chains 40, Residues 204, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9321 restraints for refining 3971 atoms. 8545 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1947 (Rfree = 0.000) for 3971 atoms. Found 23 (29 requested) and removed 15 (14 requested) atoms. Cycle 37: After refmac, R = 0.1833 (Rfree = 0.000) for 3974 atoms. Found 18 (30 requested) and removed 17 (15 requested) atoms. Cycle 38: After refmac, R = 0.1807 (Rfree = 0.000) for 3973 atoms. Found 20 (30 requested) and removed 17 (15 requested) atoms. Cycle 39: After refmac, R = 0.1758 (Rfree = 0.000) for 3975 atoms. Found 20 (30 requested) and removed 17 (15 requested) atoms. Cycle 40: After refmac, R = 0.1749 (Rfree = 0.000) for 3976 atoms. Found 25 (30 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 4108 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 4124 seeds are put forward Round 1: 195 peptides, 37 chains. Longest chain 12 peptides. Score 0.339 Round 2: 203 peptides, 34 chains. Longest chain 15 peptides. Score 0.407 Round 3: 201 peptides, 33 chains. Longest chain 13 peptides. Score 0.415 Round 4: 194 peptides, 32 chains. Longest chain 11 peptides. Score 0.406 Round 5: 200 peptides, 34 chains. Longest chain 11 peptides. Score 0.398 Taking the results from Round 3 Chains 33, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6884 reflections ( 99.41 % complete ) and 9620 restraints for refining 3969 atoms. 8981 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1944 (Rfree = 0.000) for 3969 atoms. Found 19 (29 requested) and removed 30 (14 requested) atoms. Cycle 42: After refmac, R = 0.1953 (Rfree = 0.000) for 3955 atoms. Found 29 (29 requested) and removed 17 (14 requested) atoms. Cycle 43: After refmac, R = 0.2035 (Rfree = 0.000) for 3965 atoms. Found 29 (29 requested) and removed 18 (14 requested) atoms. Cycle 44: After refmac, R = 0.1996 (Rfree = 0.000) for 3974 atoms. Found 30 (30 requested) and removed 20 (15 requested) atoms. Cycle 45: After refmac, R = 0.1933 (Rfree = 0.000) for 3983 atoms. Found 30 (30 requested) and removed 16 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 4105 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4119 seeds are put forward Round 1: 165 peptides, 36 chains. Longest chain 7 peptides. Score 0.247 Round 2: 194 peptides, 38 chains. Longest chain 10 peptides. Score 0.321 Round 3: 185 peptides, 33 chains. Longest chain 11 peptides. Score 0.363 Round 4: 189 peptides, 33 chains. Longest chain 11 peptides. Score 0.376 Round 5: 188 peptides, 34 chains. Longest chain 10 peptides. Score 0.358 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 156, 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 1vkh-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6884 reflections ( 99.41 % complete ) and 9599 restraints for refining 3971 atoms. 9008 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2063 (Rfree = 0.000) for 3971 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2096 (Rfree = 0.000) for 3946 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.2026 (Rfree = 0.000) for 3927 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1947 (Rfree = 0.000) for 3910 atoms. TimeTaking 59.85