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 2fur-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fur-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fur-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-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/2fur-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-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 19:28:07 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/2fur-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-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 265 and 0 Target number of residues in the AU: 265 Target solvent content: 0.6475 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 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: 55.473 3.400 Wilson plot Bfac: 76.06 5955 reflections ( 99.65 % complete ) and 0 restraints for refining 3710 atoms. Observations/parameters ratio is 0.40 ------------------------------------------------------ Starting model: R = 0.3141 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2806 (Rfree = 0.000) for 3710 atoms. Found 16 (28 requested) and removed 25 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.41 3.70 Search for helices and strands: 0 residues in 0 chains, 3760 seeds are put forward NCS extension: 0 residues added, 3760 seeds are put forward Round 1: 170 peptides, 33 chains. Longest chain 12 peptides. Score 0.336 Round 2: 250 peptides, 36 chains. Longest chain 19 peptides. Score 0.576 Round 3: 263 peptides, 31 chains. Longest chain 24 peptides. Score 0.672 Round 4: 272 peptides, 31 chains. Longest chain 29 peptides. Score 0.694 Round 5: 270 peptides, 26 chains. Longest chain 22 peptides. Score 0.740 Taking the results from Round 5 Chains 28, Residues 244, Estimated correctness of the model 67.6 % 1 chains (16 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6483 restraints for refining 3039 atoms. 5471 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2726 (Rfree = 0.000) for 3039 atoms. Found 11 (22 requested) and removed 23 (11 requested) atoms. Cycle 2: After refmac, R = 0.2401 (Rfree = 0.000) for 2949 atoms. Found 10 (22 requested) and removed 17 (11 requested) atoms. Cycle 3: After refmac, R = 0.2296 (Rfree = 0.000) for 2919 atoms. Found 6 (21 requested) and removed 19 (11 requested) atoms. Cycle 4: After refmac, R = 0.2164 (Rfree = 0.000) for 2891 atoms. Found 6 (20 requested) and removed 18 (10 requested) atoms. Cycle 5: After refmac, R = 0.2225 (Rfree = 0.000) for 2872 atoms. Found 2 (19 requested) and removed 14 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 2932 seeds are put forward NCS extension: 16 residues added (5 deleted due to clashes), 2948 seeds are put forward Round 1: 246 peptides, 38 chains. Longest chain 14 peptides. Score 0.537 Round 2: 270 peptides, 32 chains. Longest chain 21 peptides. Score 0.678 Round 3: 259 peptides, 31 chains. Longest chain 28 peptides. Score 0.662 Round 4: 274 peptides, 32 chains. Longest chain 24 peptides. Score 0.688 Round 5: 276 peptides, 28 chains. Longest chain 31 peptides. Score 0.733 Taking the results from Round 5 Chains 31, Residues 248, Estimated correctness of the model 66.0 % 2 chains (32 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 177 A 29 chains (249 residues) following loop building 1 chains (39 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 5955 reflections ( 99.65 % complete ) and 6335 restraints for refining 3040 atoms. 5231 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2515 (Rfree = 0.000) for 3040 atoms. Found 18 (20 requested) and removed 27 (11 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2357 (Rfree = 0.000) for 3004 atoms. Found 13 (19 requested) and removed 16 (11 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2146 (Rfree = 0.000) for 2991 atoms. Found 7 (19 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2050 (Rfree = 0.000) for 2978 atoms. Found 4 (18 requested) and removed 13 (11 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2000 (Rfree = 0.000) for 2965 atoms. Found 6 (18 requested) and removed 14 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.43 3.72 Search for helices and strands: 0 residues in 0 chains, 3029 seeds are put forward NCS extension: 22 residues added (13 deleted due to clashes), 3051 seeds are put forward Round 1: 234 peptides, 34 chains. Longest chain 17 peptides. Score 0.554 Round 2: 259 peptides, 31 chains. Longest chain 19 peptides. Score 0.662 Round 3: 264 peptides, 33 chains. Longest chain 30 peptides. Score 0.652 Round 4: 264 peptides, 29 chains. Longest chain 30 peptides. Score 0.696 Round 5: 270 peptides, 32 chains. Longest chain 31 peptides. Score 0.678 Taking the results from Round 4 Chains 30, Residues 235, Estimated correctness of the model 56.8 % 2 chains (38 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6461 restraints for refining 3039 atoms. 5404 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2198 (Rfree = 0.000) for 3039 atoms. Found 11 (18 requested) and removed 21 (11 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2022 (Rfree = 0.000) for 3020 atoms. Found 4 (18 requested) and removed 14 (11 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.1983 (Rfree = 0.000) for 3003 atoms. Found 1 (18 requested) and removed 12 (11 requested) atoms. Cycle 14: After refmac, R = 0.1939 (Rfree = 0.000) for 2988 atoms. Found 4 (18 requested) and removed 13 (11 requested) atoms. Cycle 15: After refmac, R = 0.1893 (Rfree = 0.000) for 2974 atoms. Found 3 (18 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.42 3.71 Search for helices and strands: 0 residues in 0 chains, 3056 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3072 seeds are put forward Round 1: 205 peptides, 34 chains. Longest chain 14 peptides. Score 0.456 Round 2: 250 peptides, 30 chains. Longest chain 17 peptides. Score 0.651 Round 3: 263 peptides, 30 chains. Longest chain 21 peptides. Score 0.683 Round 4: 248 peptides, 30 chains. Longest chain 21 peptides. Score 0.646 Round 5: 238 peptides, 28 chains. Longest chain 22 peptides. Score 0.643 Taking the results from Round 3 Chains 32, Residues 233, Estimated correctness of the model 53.4 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5955 reflections ( 99.65 % complete ) and 6715 restraints for refining 3041 atoms. 5767 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2114 (Rfree = 0.000) for 3041 atoms. Found 9 (18 requested) and removed 26 (11 requested) atoms. Cycle 17: After refmac, R = 0.1979 (Rfree = 0.000) for 3015 atoms. Found 3 (18 requested) and removed 14 (11 requested) atoms. Cycle 18: After refmac, R = 0.1926 (Rfree = 0.000) for 3003 atoms. Found 4 (18 requested) and removed 15 (11 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1788 (Rfree = 0.000) for 2988 atoms. Found 3 (18 requested) and removed 11 (11 requested) atoms. Cycle 20: After refmac, R = 0.1650 (Rfree = 0.000) for 2978 atoms. Found 4 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3075 seeds are put forward NCS extension: 33 residues added (1 deleted due to clashes), 3108 seeds are put forward Round 1: 210 peptides, 34 chains. Longest chain 15 peptides. Score 0.474 Round 2: 244 peptides, 31 chains. Longest chain 20 peptides. Score 0.623 Round 3: 246 peptides, 30 chains. Longest chain 23 peptides. Score 0.641 Round 4: 231 peptides, 29 chains. Longest chain 24 peptides. Score 0.612 Round 5: 233 peptides, 26 chains. Longest chain 31 peptides. Score 0.654 Taking the results from Round 5 Chains 27, Residues 207, Estimated correctness of the model 45.3 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5955 reflections ( 99.65 % complete ) and 6720 restraints for refining 3041 atoms. 5889 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2010 (Rfree = 0.000) for 3041 atoms. Found 11 (18 requested) and removed 21 (11 requested) atoms. Cycle 22: After refmac, R = 0.1900 (Rfree = 0.000) for 3021 atoms. Found 3 (18 requested) and removed 12 (11 requested) atoms. Cycle 23: After refmac, R = 0.1864 (Rfree = 0.000) for 3004 atoms. Found 2 (18 requested) and removed 12 (11 requested) atoms. Cycle 24: After refmac, R = 0.1770 (Rfree = 0.000) for 2992 atoms. Found 2 (18 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1708 (Rfree = 0.000) for 2981 atoms. Found 2 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.38 3.66 Search for helices and strands: 0 residues in 0 chains, 3075 seeds are put forward NCS extension: 54 residues added (4 deleted due to clashes), 3129 seeds are put forward Round 1: 183 peptides, 28 chains. Longest chain 15 peptides. Score 0.471 Round 2: 202 peptides, 29 chains. Longest chain 19 peptides. Score 0.522 Round 3: 209 peptides, 28 chains. Longest chain 24 peptides. Score 0.559 Round 4: 211 peptides, 28 chains. Longest chain 17 peptides. Score 0.565 Round 5: 217 peptides, 29 chains. Longest chain 22 peptides. Score 0.570 Taking the results from Round 5 Chains 29, Residues 188, Estimated correctness of the model 18.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 6978 restraints for refining 3041 atoms. 6255 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1988 (Rfree = 0.000) for 3041 atoms. Found 14 (18 requested) and removed 15 (11 requested) atoms. Cycle 27: After refmac, R = 0.1844 (Rfree = 0.000) for 3031 atoms. Found 6 (18 requested) and removed 17 (11 requested) atoms. Cycle 28: After refmac, R = 0.1796 (Rfree = 0.000) for 3017 atoms. Found 4 (18 requested) and removed 13 (11 requested) atoms. Cycle 29: After refmac, R = 0.1716 (Rfree = 0.000) for 3004 atoms. Found 6 (18 requested) and removed 12 (11 requested) atoms. Cycle 30: After refmac, R = 0.1634 (Rfree = 0.000) for 2993 atoms. Found 3 (18 requested) and removed 12 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.36 3.64 Search for helices and strands: 0 residues in 0 chains, 3060 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 3083 seeds are put forward Round 1: 193 peptides, 37 chains. Longest chain 10 peptides. Score 0.361 Round 2: 223 peptides, 32 chains. Longest chain 18 peptides. Score 0.547 Round 3: 215 peptides, 30 chains. Longest chain 18 peptides. Score 0.550 Round 4: 215 peptides, 32 chains. Longest chain 18 peptides. Score 0.521 Round 5: 219 peptides, 27 chains. Longest chain 18 peptides. Score 0.603 Taking the results from Round 5 Chains 28, Residues 192, Estimated correctness of the model 29.7 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5955 reflections ( 99.65 % complete ) and 6775 restraints for refining 3041 atoms. 5997 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1981 (Rfree = 0.000) for 3041 atoms. Found 14 (18 requested) and removed 13 (11 requested) atoms. Cycle 32: After refmac, R = 0.1855 (Rfree = 0.000) for 3035 atoms. Found 8 (18 requested) and removed 14 (11 requested) atoms. Cycle 33: After refmac, R = 0.1903 (Rfree = 0.000) for 3025 atoms. Found 10 (18 requested) and removed 12 (11 requested) atoms. Cycle 34: After refmac, R = 0.1853 (Rfree = 0.000) for 3018 atoms. Found 8 (18 requested) and removed 12 (11 requested) atoms. Cycle 35: After refmac, R = 0.1704 (Rfree = 0.000) for 3010 atoms. Found 11 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.39 3.67 Search for helices and strands: 0 residues in 0 chains, 3105 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 3127 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 11 peptides. Score 0.383 Round 2: 183 peptides, 28 chains. Longest chain 18 peptides. Score 0.471 Round 3: 200 peptides, 29 chains. Longest chain 27 peptides. Score 0.515 Round 4: 184 peptides, 27 chains. Longest chain 20 peptides. Score 0.490 Round 5: 192 peptides, 27 chains. Longest chain 21 peptides. Score 0.518 Taking the results from Round 5 Chains 28, Residues 165, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 5955 reflections ( 99.65 % complete ) and 6845 restraints for refining 3041 atoms. 6128 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2068 (Rfree = 0.000) for 3041 atoms. Found 8 (18 requested) and removed 18 (11 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.1893 (Rfree = 0.000) for 3018 atoms. Found 10 (18 requested) and removed 12 (11 requested) atoms. Cycle 38: After refmac, R = 0.1962 (Rfree = 0.000) for 3012 atoms. Found 9 (18 requested) and removed 14 (11 requested) atoms. Cycle 39: After refmac, R = 0.1837 (Rfree = 0.000) for 3007 atoms. Found 6 (18 requested) and removed 15 (11 requested) atoms. Cycle 40: After refmac, R = 0.1842 (Rfree = 0.000) for 2993 atoms. Found 13 (18 requested) and removed 11 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 3.65 Search for helices and strands: 0 residues in 0 chains, 3080 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 3108 seeds are put forward Round 1: 154 peptides, 31 chains. Longest chain 8 peptides. Score 0.304 Round 2: 178 peptides, 29 chains. Longest chain 14 peptides. Score 0.436 Round 3: 185 peptides, 30 chains. Longest chain 13 peptides. Score 0.446 Round 4: 184 peptides, 30 chains. Longest chain 14 peptides. Score 0.442 Round 5: 194 peptides, 28 chains. Longest chain 15 peptides. Score 0.509 Taking the results from Round 5 Chains 28, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5955 reflections ( 99.65 % complete ) and 7023 restraints for refining 3041 atoms. 6387 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1976 (Rfree = 0.000) for 3041 atoms. Found 17 (18 requested) and removed 13 (11 requested) atoms. Cycle 42: After refmac, R = 0.2019 (Rfree = 0.000) for 3039 atoms. Found 14 (18 requested) and removed 14 (11 requested) atoms. Cycle 43: After refmac, R = 0.1840 (Rfree = 0.000) for 3037 atoms. Found 9 (18 requested) and removed 11 (11 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1791 (Rfree = 0.000) for 3031 atoms. Found 6 (18 requested) and removed 12 (11 requested) atoms. Cycle 45: After refmac, R = 0.1735 (Rfree = 0.000) for 3024 atoms. Found 5 (18 requested) and removed 13 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.68 Search for helices and strands: 0 residues in 0 chains, 3106 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 3132 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 8 peptides. Score 0.263 Round 2: 184 peptides, 30 chains. Longest chain 13 peptides. Score 0.442 Round 3: 178 peptides, 31 chains. Longest chain 12 peptides. Score 0.403 Round 4: 180 peptides, 28 chains. Longest chain 12 peptides. Score 0.460 Round 5: 170 peptides, 28 chains. Longest chain 12 peptides. Score 0.422 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 152, 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 2fur-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5955 reflections ( 99.65 % complete ) and 7095 restraints for refining 3041 atoms. 6515 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1836 (Rfree = 0.000) for 3041 atoms. Found 0 (18 requested) and removed 10 (11 requested) atoms. Cycle 47: After refmac, R = 0.1736 (Rfree = 0.000) for 3026 atoms. Found 0 (18 requested) and removed 1 (11 requested) atoms. Cycle 48: After refmac, R = 0.1762 (Rfree = 0.000) for 3024 atoms. Found 0 (18 requested) and removed 2 (11 requested) atoms. Cycle 49: After refmac, R = 0.1549 (Rfree = 0.000) for 3022 atoms. Found 0 (18 requested) and removed 3 (11 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:24:07 GMT 2018 Job finished. TimeTaking 56.17