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 1vlm-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vlm-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-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/1vlm-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-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/1vlm-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vlm-3.8-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 287 and 0 Target number of residues in the AU: 287 Target solvent content: 0.6439 Checking the provided sequence file Detected sequence length: 219 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 438 Adjusted target solvent content: 0.46 Input MTZ file: 1vlm-3.8-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: 18 Cell parameters: 65.648 70.734 93.922 90.000 90.000 90.000 Input sequence file: 1vlm-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 3504 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: 93.922 3.800 Wilson plot Bfac: 74.33 4626 reflections ( 99.66 % complete ) and 0 restraints for refining 3868 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3239 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3235 (Rfree = 0.000) for 3868 atoms. Found 21 (21 requested) and removed 29 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 3914 seeds are put forward NCS extension: 0 residues added, 3914 seeds are put forward Round 1: 117 peptides, 23 chains. Longest chain 14 peptides. Score 0.284 Round 2: 176 peptides, 34 chains. Longest chain 10 peptides. Score 0.334 Round 3: 202 peptides, 34 chains. Longest chain 12 peptides. Score 0.431 Round 4: 212 peptides, 32 chains. Longest chain 13 peptides. Score 0.494 Round 5: 215 peptides, 34 chains. Longest chain 14 peptides. Score 0.475 Taking the results from Round 4 Chains 32, Residues 180, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7072 restraints for refining 3076 atoms. 6348 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2725 (Rfree = 0.000) for 3076 atoms. Found 8 (16 requested) and removed 26 (8 requested) atoms. Cycle 2: After refmac, R = 0.2657 (Rfree = 0.000) for 3002 atoms. Found 5 (16 requested) and removed 19 (8 requested) atoms. Cycle 3: After refmac, R = 0.2480 (Rfree = 0.000) for 2957 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2400 (Rfree = 0.000) for 2928 atoms. Found 7 (16 requested) and removed 14 (8 requested) atoms. Cycle 5: After refmac, R = 0.2314 (Rfree = 0.000) for 2908 atoms. Found 4 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 2997 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 3013 seeds are put forward Round 1: 175 peptides, 34 chains. Longest chain 8 peptides. Score 0.330 Round 2: 213 peptides, 34 chains. Longest chain 16 peptides. Score 0.468 Round 3: 231 peptides, 37 chains. Longest chain 17 peptides. Score 0.485 Round 4: 214 peptides, 32 chains. Longest chain 14 peptides. Score 0.500 Round 5: 224 peptides, 34 chains. Longest chain 13 peptides. Score 0.504 Taking the results from Round 5 Chains 34, Residues 190, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6712 restraints for refining 2931 atoms. 5986 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2254 (Rfree = 0.000) for 2931 atoms. Found 12 (16 requested) and removed 71 (8 requested) atoms. Cycle 7: After refmac, R = 0.2068 (Rfree = 0.000) for 2854 atoms. Found 9 (15 requested) and removed 34 (7 requested) atoms. Cycle 8: After refmac, R = 0.1923 (Rfree = 0.000) for 2814 atoms. Found 12 (15 requested) and removed 20 (7 requested) atoms. Cycle 9: After refmac, R = 0.1883 (Rfree = 0.000) for 2791 atoms. Found 7 (15 requested) and removed 13 (7 requested) atoms. Cycle 10: After refmac, R = 0.1925 (Rfree = 0.000) for 2781 atoms. Found 12 (15 requested) and removed 16 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.55 3.74 Search for helices and strands: 0 residues in 0 chains, 2915 seeds are put forward NCS extension: 15 residues added (2 deleted due to clashes), 2930 seeds are put forward Round 1: 184 peptides, 37 chains. Longest chain 10 peptides. Score 0.316 Round 2: 213 peptides, 37 chains. Longest chain 14 peptides. Score 0.424 Round 3: 206 peptides, 36 chains. Longest chain 11 peptides. Score 0.414 Round 4: 218 peptides, 37 chains. Longest chain 14 peptides. Score 0.441 Round 5: 219 peptides, 34 chains. Longest chain 17 peptides. Score 0.488 Taking the results from Round 5 Chains 34, Residues 185, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6825 restraints for refining 2977 atoms. 6119 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2119 (Rfree = 0.000) for 2977 atoms. Found 16 (16 requested) and removed 56 (8 requested) atoms. Cycle 12: After refmac, R = 0.1958 (Rfree = 0.000) for 2916 atoms. Found 5 (16 requested) and removed 30 (8 requested) atoms. Cycle 13: After refmac, R = 0.1941 (Rfree = 0.000) for 2887 atoms. Found 6 (15 requested) and removed 19 (7 requested) atoms. Cycle 14: After refmac, R = 0.1955 (Rfree = 0.000) for 2870 atoms. Found 3 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.1967 (Rfree = 0.000) for 2858 atoms. Found 4 (15 requested) and removed 10 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 30 residues added (3 deleted due to clashes), 2953 seeds are put forward Round 1: 198 peptides, 40 chains. Longest chain 10 peptides. Score 0.322 Round 2: 223 peptides, 40 chains. Longest chain 13 peptides. Score 0.414 Round 3: 223 peptides, 38 chains. Longest chain 14 peptides. Score 0.444 Round 4: 214 peptides, 35 chains. Longest chain 14 peptides. Score 0.457 Round 5: 208 peptides, 36 chains. Longest chain 12 peptides. Score 0.421 Taking the results from Round 4 Chains 35, Residues 179, Estimated correctness of the model 0.0 % 3 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6829 restraints for refining 3053 atoms. 6074 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2213 (Rfree = 0.000) for 3053 atoms. Found 16 (16 requested) and removed 49 (8 requested) atoms. Cycle 17: After refmac, R = 0.2029 (Rfree = 0.000) for 2993 atoms. Found 12 (16 requested) and removed 36 (8 requested) atoms. Cycle 18: After refmac, R = 0.1999 (Rfree = 0.000) for 2944 atoms. Found 7 (16 requested) and removed 26 (8 requested) atoms. Cycle 19: After refmac, R = 0.1847 (Rfree = 0.000) for 2913 atoms. Found 5 (16 requested) and removed 14 (8 requested) atoms. Cycle 20: After refmac, R = 0.1901 (Rfree = 0.000) for 2900 atoms. Found 4 (15 requested) and removed 12 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.56 3.76 Search for helices and strands: 0 residues in 0 chains, 2983 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 3001 seeds are put forward Round 1: 155 peptides, 34 chains. Longest chain 7 peptides. Score 0.249 Round 2: 180 peptides, 28 chains. Longest chain 19 peptides. Score 0.445 Round 3: 160 peptides, 30 chains. Longest chain 9 peptides. Score 0.338 Round 4: 180 peptides, 29 chains. Longest chain 13 peptides. Score 0.429 Round 5: 171 peptides, 31 chains. Longest chain 11 peptides. Score 0.364 Taking the results from Round 2 Chains 29, Residues 152, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6629 restraints for refining 2915 atoms. 6010 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2037 (Rfree = 0.000) for 2915 atoms. Found 4 (16 requested) and removed 33 (8 requested) atoms. Cycle 22: After refmac, R = 0.1921 (Rfree = 0.000) for 2870 atoms. Found 10 (15 requested) and removed 12 (7 requested) atoms. Cycle 23: After refmac, R = 0.2033 (Rfree = 0.000) for 2856 atoms. Found 10 (15 requested) and removed 19 (7 requested) atoms. Cycle 24: After refmac, R = 0.2042 (Rfree = 0.000) for 2838 atoms. Found 15 (15 requested) and removed 22 (7 requested) atoms. Cycle 25: After refmac, R = 0.1823 (Rfree = 0.000) for 2823 atoms. Found 0 (15 requested) and removed 11 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.77 Search for helices and strands: 0 residues in 0 chains, 2923 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 2944 seeds are put forward Round 1: 159 peptides, 35 chains. Longest chain 9 peptides. Score 0.249 Round 2: 192 peptides, 35 chains. Longest chain 10 peptides. Score 0.379 Round 3: 207 peptides, 35 chains. Longest chain 14 peptides. Score 0.433 Round 4: 191 peptides, 35 chains. Longest chain 14 peptides. Score 0.375 Round 5: 207 peptides, 35 chains. Longest chain 16 peptides. Score 0.433 Taking the results from Round 5 Chains 35, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6818 restraints for refining 3003 atoms. 6165 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2093 (Rfree = 0.000) for 3003 atoms. Found 12 (16 requested) and removed 40 (8 requested) atoms. Cycle 27: After refmac, R = 0.1937 (Rfree = 0.000) for 2948 atoms. Found 2 (16 requested) and removed 25 (8 requested) atoms. Cycle 28: After refmac, R = 0.1867 (Rfree = 0.000) for 2918 atoms. Found 2 (16 requested) and removed 18 (8 requested) atoms. Cycle 29: After refmac, R = 0.1871 (Rfree = 0.000) for 2898 atoms. Found 5 (15 requested) and removed 18 (7 requested) atoms. Cycle 30: After refmac, R = 0.1883 (Rfree = 0.000) for 2884 atoms. Found 2 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.54 3.73 Search for helices and strands: 0 residues in 0 chains, 2973 seeds are put forward NCS extension: 29 residues added (2 deleted due to clashes), 3002 seeds are put forward Round 1: 153 peptides, 31 chains. Longest chain 11 peptides. Score 0.293 Round 2: 180 peptides, 32 chains. Longest chain 9 peptides. Score 0.382 Round 3: 186 peptides, 33 chains. Longest chain 11 peptides. Score 0.388 Round 4: 190 peptides, 32 chains. Longest chain 12 peptides. Score 0.419 Round 5: 196 peptides, 33 chains. Longest chain 13 peptides. Score 0.425 Taking the results from Round 5 Chains 33, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 6957 restraints for refining 3018 atoms. 6338 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2246 (Rfree = 0.000) for 3018 atoms. Found 16 (16 requested) and removed 47 (8 requested) atoms. Cycle 32: After refmac, R = 0.2256 (Rfree = 0.000) for 2978 atoms. Found 8 (16 requested) and removed 26 (8 requested) atoms. Cycle 33: After refmac, R = 0.2179 (Rfree = 0.000) for 2958 atoms. Found 4 (16 requested) and removed 20 (8 requested) atoms. Cycle 34: After refmac, R = 0.2144 (Rfree = 0.000) for 2942 atoms. Found 3 (16 requested) and removed 13 (8 requested) atoms. Cycle 35: After refmac, R = 0.2112 (Rfree = 0.000) for 2929 atoms. Found 2 (16 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.58 3.78 Search for helices and strands: 0 residues in 0 chains, 3009 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 3028 seeds are put forward Round 1: 141 peptides, 30 chains. Longest chain 8 peptides. Score 0.260 Round 2: 160 peptides, 26 chains. Longest chain 11 peptides. Score 0.404 Round 3: 148 peptides, 27 chains. Longest chain 10 peptides. Score 0.341 Round 4: 160 peptides, 29 chains. Longest chain 10 peptides. Score 0.355 Round 5: 163 peptides, 30 chains. Longest chain 10 peptides. Score 0.350 Taking the results from Round 2 Chains 26, Residues 134, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7181 restraints for refining 3051 atoms. 6624 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2087 (Rfree = 0.000) for 3051 atoms. Found 16 (16 requested) and removed 47 (8 requested) atoms. Cycle 37: After refmac, R = 0.2025 (Rfree = 0.000) for 3009 atoms. Found 9 (16 requested) and removed 21 (8 requested) atoms. Cycle 38: After refmac, R = 0.1976 (Rfree = 0.000) for 2994 atoms. Found 6 (16 requested) and removed 18 (8 requested) atoms. Cycle 39: After refmac, R = 0.1964 (Rfree = 0.000) for 2980 atoms. Failed to save intermediate PDB Found 3 (16 requested) and removed 20 (8 requested) atoms. Cycle 40: After refmac, R = 0.1989 (Rfree = 0.000) for 2962 atoms. Found 3 (16 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.72 Search for helices and strands: 0 residues in 0 chains, 3041 seeds are put forward NCS extension: 11 residues added (2 deleted due to clashes), 3052 seeds are put forward Round 1: 118 peptides, 25 chains. Longest chain 7 peptides. Score 0.251 Round 2: 151 peptides, 29 chains. Longest chain 10 peptides. Score 0.319 Round 3: 162 peptides, 29 chains. Longest chain 10 peptides. Score 0.363 Round 4: 174 peptides, 29 chains. Longest chain 13 peptides. Score 0.408 Round 5: 167 peptides, 27 chains. Longest chain 12 peptides. Score 0.414 Taking the results from Round 5 Chains 27, Residues 140, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4626 reflections ( 99.66 % complete ) and 7188 restraints for refining 3057 atoms. 6636 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2169 (Rfree = 0.000) for 3057 atoms. Found 6 (16 requested) and removed 40 (8 requested) atoms. Cycle 42: After refmac, R = 0.2057 (Rfree = 0.000) for 3016 atoms. Found 6 (16 requested) and removed 14 (8 requested) atoms. Cycle 43: After refmac, R = 0.1993 (Rfree = 0.000) for 3003 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. Cycle 44: After refmac, R = 0.2030 (Rfree = 0.000) for 2990 atoms. Found 10 (16 requested) and removed 19 (8 requested) atoms. Cycle 45: After refmac, R = 0.1896 (Rfree = 0.000) for 2977 atoms. Found 8 (16 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.50 3.69 Search for helices and strands: 0 residues in 0 chains, 3056 seeds are put forward NCS extension: 0 residues added, 3056 seeds are put forward Round 1: 110 peptides, 24 chains. Longest chain 8 peptides. Score 0.234 Round 2: 122 peptides, 22 chains. Longest chain 11 peptides. Score 0.324 Round 3: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.332 Round 4: 124 peptides, 21 chains. Longest chain 13 peptides. Score 0.350 Round 5: 123 peptides, 20 chains. Longest chain 10 peptides. Score 0.364 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 103, 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 1vlm-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4626 reflections ( 99.66 % complete ) and 7317 restraints for refining 3055 atoms. 6925 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2072 (Rfree = 0.000) for 3055 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2165 (Rfree = 0.000) for 3027 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1927 (Rfree = 0.000) for 3003 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.1983 (Rfree = 0.000) for 2979 atoms. TimeTaking 50.27