Tue 25 Dec 19:27:57 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2h1q-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-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/2h1q-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-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 ============================================================ Tue 25 Dec 19:28:06 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2h1q-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 405 and 0 Target number of residues in the AU: 405 Target solvent content: 0.6538 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-3.4-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-3.4-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 3.400 Wilson plot Bfac: 80.39 8694 reflections ( 99.63 % complete ) and 0 restraints for refining 4763 atoms. Observations/parameters ratio is 0.46 ------------------------------------------------------ Starting model: R = 0.3387 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3284 (Rfree = 0.000) for 4763 atoms. Found 35 (35 requested) and removed 219 (17 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.46 3.28 Search for helices and strands: 0 residues in 0 chains, 4638 seeds are put forward NCS extension: 0 residues added, 4638 seeds are put forward Round 1: 107 peptides, 22 chains. Longest chain 11 peptides. Score 0.239 Round 2: 154 peptides, 30 chains. Longest chain 10 peptides. Score 0.280 Round 3: 196 peptides, 37 chains. Longest chain 14 peptides. Score 0.315 Round 4: 198 peptides, 36 chains. Longest chain 10 peptides. Score 0.333 Round 5: 200 peptides, 35 chains. Longest chain 14 peptides. Score 0.351 Taking the results from Round 5 Chains 35, Residues 165, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9512 restraints for refining 3915 atoms. 8835 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2934 (Rfree = 0.000) for 3915 atoms. Found 26 (29 requested) and removed 75 (14 requested) atoms. Cycle 2: After refmac, R = 0.2774 (Rfree = 0.000) for 3831 atoms. Found 20 (29 requested) and removed 52 (14 requested) atoms. Cycle 3: After refmac, R = 0.2646 (Rfree = 0.000) for 3783 atoms. Found 13 (28 requested) and removed 36 (14 requested) atoms. Cycle 4: After refmac, R = 0.2594 (Rfree = 0.000) for 3744 atoms. Found 16 (28 requested) and removed 31 (14 requested) atoms. Cycle 5: After refmac, R = 0.2441 (Rfree = 0.000) for 3718 atoms. Found 13 (28 requested) and removed 23 (14 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3806 seeds are put forward NCS extension: 0 residues added, 3806 seeds are put forward Round 1: 202 peptides, 41 chains. Longest chain 10 peptides. Score 0.284 Round 2: 220 peptides, 37 chains. Longest chain 19 peptides. Score 0.381 Round 3: 223 peptides, 37 chains. Longest chain 18 peptides. Score 0.389 Round 4: 226 peptides, 33 chains. Longest chain 24 peptides. Score 0.442 Round 5: 236 peptides, 33 chains. Longest chain 19 peptides. Score 0.466 Taking the results from Round 5 Chains 33, Residues 203, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8835 restraints for refining 3750 atoms. 8046 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2459 (Rfree = 0.000) for 3750 atoms. Found 24 (28 requested) and removed 44 (14 requested) atoms. Cycle 7: After refmac, R = 0.2358 (Rfree = 0.000) for 3710 atoms. Found 19 (28 requested) and removed 42 (14 requested) atoms. Cycle 8: After refmac, R = 0.2352 (Rfree = 0.000) for 3680 atoms. Found 12 (27 requested) and removed 20 (13 requested) atoms. Cycle 9: After refmac, R = 0.2426 (Rfree = 0.000) for 3656 atoms. Found 25 (27 requested) and removed 19 (13 requested) atoms. Cycle 10: After refmac, R = 0.2144 (Rfree = 0.000) for 3651 atoms. Found 6 (27 requested) and removed 20 (13 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 3750 seeds are put forward NCS extension: 28 residues added (1 deleted due to clashes), 3778 seeds are put forward Round 1: 221 peptides, 42 chains. Longest chain 10 peptides. Score 0.325 Round 2: 238 peptides, 37 chains. Longest chain 17 peptides. Score 0.427 Round 3: 247 peptides, 42 chains. Longest chain 15 peptides. Score 0.395 Round 4: 256 peptides, 39 chains. Longest chain 18 peptides. Score 0.450 Round 5: 267 peptides, 41 chains. Longest chain 27 peptides. Score 0.455 Taking the results from Round 5 Chains 41, Residues 226, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 8839 restraints for refining 3824 atoms. 7976 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2378 (Rfree = 0.000) for 3824 atoms. Found 20 (28 requested) and removed 37 (14 requested) atoms. Cycle 12: After refmac, R = 0.2410 (Rfree = 0.000) for 3791 atoms. Found 17 (28 requested) and removed 24 (14 requested) atoms. Cycle 13: After refmac, R = 0.2359 (Rfree = 0.000) for 3770 atoms. Found 13 (28 requested) and removed 30 (14 requested) atoms. Cycle 14: After refmac, R = 0.2136 (Rfree = 0.000) for 3741 atoms. Found 6 (28 requested) and removed 19 (14 requested) atoms. Cycle 15: After refmac, R = 0.2151 (Rfree = 0.000) for 3724 atoms. Found 5 (28 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.45 3.27 Search for helices and strands: 0 residues in 0 chains, 3867 seeds are put forward NCS extension: 31 residues added (4 deleted due to clashes), 3898 seeds are put forward Round 1: 226 peptides, 43 chains. Longest chain 11 peptides. Score 0.327 Round 2: 253 peptides, 40 chains. Longest chain 14 peptides. Score 0.432 Round 3: 239 peptides, 38 chains. Longest chain 12 peptides. Score 0.419 Round 4: 241 peptides, 37 chains. Longest chain 12 peptides. Score 0.435 Round 5: 232 peptides, 35 chains. Longest chain 14 peptides. Score 0.435 Taking the results from Round 5 Chains 35, Residues 197, Estimated correctness of the model 0.0 % 2 chains (7 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 8694 reflections ( 99.63 % complete ) and 9156 restraints for refining 3882 atoms. 8392 conditional restraints added. Observations/parameters ratio is 0.56 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2388 (Rfree = 0.000) for 3882 atoms. Found 27 (29 requested) and removed 43 (14 requested) atoms. Cycle 17: After refmac, R = 0.2227 (Rfree = 0.000) for 3859 atoms. Found 10 (29 requested) and removed 26 (14 requested) atoms. Cycle 18: After refmac, R = 0.2279 (Rfree = 0.000) for 3834 atoms. Found 18 (29 requested) and removed 25 (14 requested) atoms. Cycle 19: After refmac, R = 0.2186 (Rfree = 0.000) for 3820 atoms. Found 18 (28 requested) and removed 26 (14 requested) atoms. Cycle 20: After refmac, R = 0.2174 (Rfree = 0.000) for 3807 atoms. Found 11 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3909 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 3926 seeds are put forward Round 1: 216 peptides, 41 chains. Longest chain 12 peptides. Score 0.323 Round 2: 236 peptides, 39 chains. Longest chain 15 peptides. Score 0.400 Round 3: 229 peptides, 36 chains. Longest chain 13 peptides. Score 0.416 Round 4: 244 peptides, 40 chains. Longest chain 14 peptides. Score 0.409 Round 5: 252 peptides, 37 chains. Longest chain 13 peptides. Score 0.462 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 ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9201 restraints for refining 3927 atoms. 8378 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2360 (Rfree = 0.000) for 3927 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. Cycle 22: After refmac, R = 0.2299 (Rfree = 0.000) for 3910 atoms. Found 24 (29 requested) and removed 23 (14 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2223 (Rfree = 0.000) for 3900 atoms. Found 22 (29 requested) and removed 23 (14 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2155 (Rfree = 0.000) for 3893 atoms. Found 16 (29 requested) and removed 22 (14 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2109 (Rfree = 0.000) for 3876 atoms. Found 8 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 3979 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 3992 seeds are put forward Round 1: 194 peptides, 39 chains. Longest chain 10 peptides. Score 0.285 Round 2: 209 peptides, 33 chains. Longest chain 14 peptides. Score 0.399 Round 3: 203 peptides, 32 chains. Longest chain 13 peptides. Score 0.394 Round 4: 209 peptides, 31 chains. Longest chain 17 peptides. Score 0.422 Round 5: 201 peptides, 32 chains. Longest chain 14 peptides. Score 0.389 Taking the results from Round 4 Chains 31, Residues 178, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9213 restraints for refining 3927 atoms. 8495 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2184 (Rfree = 0.000) for 3927 atoms. Found 14 (29 requested) and removed 20 (14 requested) atoms. Cycle 27: After refmac, R = 0.2088 (Rfree = 0.000) for 3911 atoms. Found 17 (29 requested) and removed 22 (14 requested) atoms. Cycle 28: After refmac, R = 0.2117 (Rfree = 0.000) for 3897 atoms. Found 16 (29 requested) and removed 21 (14 requested) atoms. Cycle 29: After refmac, R = 0.2064 (Rfree = 0.000) for 3886 atoms. Found 15 (29 requested) and removed 18 (14 requested) atoms. Cycle 30: After refmac, R = 0.2367 (Rfree = 0.000) for 3880 atoms. Found 29 (29 requested) and removed 27 (14 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 3983 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 4001 seeds are put forward Round 1: 185 peptides, 36 chains. Longest chain 11 peptides. Score 0.296 Round 2: 195 peptides, 34 chains. Longest chain 12 peptides. Score 0.349 Round 3: 198 peptides, 31 chains. Longest chain 12 peptides. Score 0.393 Round 4: 202 peptides, 33 chains. Longest chain 12 peptides. Score 0.380 Round 5: 199 peptides, 31 chains. Longest chain 12 peptides. Score 0.396 Taking the results from Round 5 Chains 31, Residues 168, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9268 restraints for refining 3927 atoms. 8613 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2118 (Rfree = 0.000) for 3927 atoms. Found 19 (29 requested) and removed 23 (14 requested) atoms. Cycle 32: After refmac, R = 0.2039 (Rfree = 0.000) for 3918 atoms. Found 14 (29 requested) and removed 24 (14 requested) atoms. Cycle 33: After refmac, R = 0.1944 (Rfree = 0.000) for 3903 atoms. Found 10 (29 requested) and removed 18 (14 requested) atoms. Cycle 34: After refmac, R = 0.1919 (Rfree = 0.000) for 3888 atoms. Found 11 (29 requested) and removed 23 (14 requested) atoms. Cycle 35: After refmac, R = 0.1833 (Rfree = 0.000) for 3874 atoms. Found 4 (29 requested) and removed 18 (14 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 3953 seeds are put forward NCS extension: 0 residues added, 3953 seeds are put forward Round 1: 180 peptides, 37 chains. Longest chain 10 peptides. Score 0.268 Round 2: 204 peptides, 37 chains. Longest chain 16 peptides. Score 0.338 Round 3: 208 peptides, 38 chains. Longest chain 12 peptides. Score 0.337 Round 4: 220 peptides, 39 chains. Longest chain 18 peptides. Score 0.358 Round 5: 222 peptides, 38 chains. Longest chain 15 peptides. Score 0.375 Taking the results from Round 5 Chains 38, Residues 184, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9330 restraints for refining 3928 atoms. 8632 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2090 (Rfree = 0.000) for 3928 atoms. Found 15 (29 requested) and removed 18 (14 requested) atoms. Cycle 37: After refmac, R = 0.2014 (Rfree = 0.000) for 3919 atoms. Found 14 (29 requested) and removed 24 (14 requested) atoms. Cycle 38: After refmac, R = 0.1939 (Rfree = 0.000) for 3902 atoms. Found 17 (29 requested) and removed 21 (14 requested) atoms. Cycle 39: After refmac, R = 0.1877 (Rfree = 0.000) for 3894 atoms. Found 10 (29 requested) and removed 20 (14 requested) atoms. Cycle 40: After refmac, R = 0.1835 (Rfree = 0.000) for 3879 atoms. Found 13 (29 requested) and removed 20 (14 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.40 3.22 Search for helices and strands: 0 residues in 0 chains, 3965 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 3994 seeds are put forward Round 1: 178 peptides, 39 chains. Longest chain 8 peptides. Score 0.237 Round 2: 193 peptides, 35 chains. Longest chain 12 peptides. Score 0.331 Round 3: 185 peptides, 34 chains. Longest chain 10 peptides. Score 0.321 Round 4: 181 peptides, 33 chains. Longest chain 10 peptides. Score 0.322 Round 5: 196 peptides, 34 chains. Longest chain 16 peptides. Score 0.352 Taking the results from Round 5 Chains 34, Residues 162, Estimated correctness of the model 0.0 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 8694 reflections ( 99.63 % complete ) and 9339 restraints for refining 3928 atoms. 8715 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2118 (Rfree = 0.000) for 3928 atoms. Found 29 (29 requested) and removed 19 (14 requested) atoms. Cycle 42: After refmac, R = 0.2065 (Rfree = 0.000) for 3929 atoms. Found 28 (29 requested) and removed 22 (14 requested) atoms. Cycle 43: After refmac, R = 0.1974 (Rfree = 0.000) for 3928 atoms. Found 29 (29 requested) and removed 21 (14 requested) atoms. Cycle 44: After refmac, R = 0.1724 (Rfree = 0.000) for 3928 atoms. Found 10 (29 requested) and removed 17 (14 requested) atoms. Cycle 45: After refmac, R = 0.1798 (Rfree = 0.000) for 3918 atoms. Found 18 (29 requested) and removed 19 (14 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.38 3.20 Search for helices and strands: 0 residues in 0 chains, 4048 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 4074 seeds are put forward Round 1: 180 peptides, 37 chains. Longest chain 9 peptides. Score 0.268 Round 2: 201 peptides, 37 chains. Longest chain 9 peptides. Score 0.329 Round 3: 175 peptides, 33 chains. Longest chain 11 peptides. Score 0.304 Round 4: 191 peptides, 35 chains. Longest chain 9 peptides. Score 0.325 Round 5: 182 peptides, 31 chains. Longest chain 12 peptides. Score 0.349 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 32, Residues 151, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 8 % Consider running further cycles of model building using 2h1q-3_warpNtrace.pdb as input Building loops using Loopy2018 32 chains (151 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8694 reflections ( 99.63 % complete ) and 9252 restraints for refining 3928 atoms. 8649 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1987 (Rfree = 0.000) for 3928 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 47: After refmac, R = 0.1962 (Rfree = 0.000) for 3904 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 48: After refmac, R = 0.1892 (Rfree = 0.000) for 3887 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Cycle 49: After refmac, R = 0.1981 (Rfree = 0.000) for 3870 atoms. Found 0 (29 requested) and removed 14 (14 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 68.58