Sun 23 Dec 22:22:44 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 2pr7-1.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-1.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pr7-1.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-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/2pr7-1.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-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 22:22:53 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/2pr7-1.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pr7-1.4-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 288 and 0 Target number of residues in the AU: 288 Target solvent content: 0.4668 Checking the provided sequence file Detected sequence length: 137 Maximum limit of NCS related copies: 16 Number of NCS-related molecules: 2 Adjusted target number of residues: 274 Adjusted target solvent content: 0.49 Input MTZ file: 2pr7-1.4-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: 1 Cell parameters: 29.149 45.153 60.777 100.722 103.858 103.308 Input sequence file: 2pr7-1.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 2192 target number of atoms Had to go as low as 0.40 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 1 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 Loops will be built when appropriate and at the last cycle Resolution range: 57.053 1.440 Wilson plot Bfac: 17.25 40620 reflections ( 79.26 % complete ) and 0 restraints for refining 2423 atoms. Observations/parameters ratio is 4.19 ------------------------------------------------------ Starting model: R = 0.3281 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2760 (Rfree = 0.000) for 2423 atoms. Found 146 (211 requested) and removed 112 (105 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.72 1.74 Round 1: 238 peptides, 17 chains. Longest chain 40 peptides. Score 0.851 Round 2: 260 peptides, 8 chains. Longest chain 59 peptides. Score 0.934 Round 3: 261 peptides, 7 chains. Longest chain 63 peptides. Score 0.940 Round 4: 259 peptides, 7 chains. Longest chain 59 peptides. Score 0.939 Round 5: 261 peptides, 7 chains. Longest chain 63 peptides. Score 0.940 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2516 restraints for refining 2322 atoms. 605 conditional restraints added. Observations/parameters ratio is 4.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2804 (Rfree = 0.000) for 2322 atoms. Found 112 (202 requested) and removed 30 (101 requested) atoms. Cycle 2: After refmac, R = 0.2500 (Rfree = 0.000) for 2403 atoms. Found 82 (210 requested) and removed 5 (105 requested) atoms. Cycle 3: After refmac, R = 0.2348 (Rfree = 0.000) for 2469 atoms. Found 78 (216 requested) and removed 5 (108 requested) atoms. Cycle 4: After refmac, R = 0.2249 (Rfree = 0.000) for 2534 atoms. Found 67 (222 requested) and removed 3 (111 requested) atoms. Cycle 5: After refmac, R = 0.2183 (Rfree = 0.000) for 2592 atoms. Found 45 (226 requested) and removed 8 (113 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.68 1.70 Round 1: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 2: 262 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 3: 262 peptides, 7 chains. Longest chain 62 peptides. Score 0.941 Round 4: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 5: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Taking the results from Round 5 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2588 restraints for refining 2479 atoms. 630 conditional restraints added. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2288 (Rfree = 0.000) for 2479 atoms. Found 113 (216 requested) and removed 21 (108 requested) atoms. Cycle 7: After refmac, R = 0.2182 (Rfree = 0.000) for 2569 atoms. Found 72 (224 requested) and removed 9 (112 requested) atoms. Cycle 8: After refmac, R = 0.2095 (Rfree = 0.000) for 2628 atoms. Found 72 (229 requested) and removed 6 (114 requested) atoms. Cycle 9: After refmac, R = 0.2051 (Rfree = 0.000) for 2688 atoms. Found 62 (235 requested) and removed 12 (117 requested) atoms. Cycle 10: After refmac, R = 0.2002 (Rfree = 0.000) for 2735 atoms. Found 60 (239 requested) and removed 9 (119 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.68 1.70 Round 1: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 2: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 3: 262 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 4: 264 peptides, 4 chains. Longest chain 135 peptides. Score 0.956 Round 5: 262 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2672 restraints for refining 2586 atoms. 714 conditional restraints added. Observations/parameters ratio is 3.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2162 (Rfree = 0.000) for 2586 atoms. Found 109 (225 requested) and removed 22 (112 requested) atoms. Cycle 12: After refmac, R = 0.2069 (Rfree = 0.000) for 2671 atoms. Found 65 (233 requested) and removed 4 (116 requested) atoms. Cycle 13: After refmac, R = 0.2002 (Rfree = 0.000) for 2729 atoms. Found 52 (238 requested) and removed 8 (119 requested) atoms. Cycle 14: After refmac, R = 0.1961 (Rfree = 0.000) for 2761 atoms. Found 57 (242 requested) and removed 7 (121 requested) atoms. Cycle 15: After refmac, R = 0.1929 (Rfree = 0.000) for 2807 atoms. Found 52 (245 requested) and removed 19 (122 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.67 1.69 Round 1: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 2: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 3: 262 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 4: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 5: 265 peptides, 5 chains. Longest chain 73 peptides. Score 0.952 Taking the results from Round 4 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2755 restraints for refining 2644 atoms. 797 conditional restraints added. Observations/parameters ratio is 3.84 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2106 (Rfree = 0.000) for 2644 atoms. Found 134 (231 requested) and removed 18 (115 requested) atoms. Cycle 17: After refmac, R = 0.2040 (Rfree = 0.000) for 2757 atoms. Found 75 (241 requested) and removed 14 (120 requested) atoms. Cycle 18: After refmac, R = 0.1981 (Rfree = 0.000) for 2812 atoms. Found 68 (246 requested) and removed 11 (123 requested) atoms. Cycle 19: After refmac, R = 0.1940 (Rfree = 0.000) for 2865 atoms. Found 68 (250 requested) and removed 13 (125 requested) atoms. Cycle 20: After refmac, R = 0.1909 (Rfree = 0.000) for 2913 atoms. Found 77 (255 requested) and removed 24 (127 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.66 1.68 Round 1: 263 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 2: 263 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 3: 262 peptides, 6 chains. Longest chain 73 peptides. Score 0.946 Round 4: 263 peptides, 6 chains. Longest chain 73 peptides. Score 0.946 Round 5: 262 peptides, 6 chains. Longest chain 73 peptides. Score 0.946 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2902 restraints for refining 2703 atoms. 969 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2077 (Rfree = 0.000) for 2703 atoms. Found 139 (236 requested) and removed 15 (118 requested) atoms. Cycle 22: After refmac, R = 0.2019 (Rfree = 0.000) for 2821 atoms. Found 69 (246 requested) and removed 17 (123 requested) atoms. Cycle 23: After refmac, R = 0.1968 (Rfree = 0.000) for 2864 atoms. Found 73 (251 requested) and removed 8 (125 requested) atoms. Cycle 24: After refmac, R = 0.1915 (Rfree = 0.000) for 2925 atoms. Found 60 (255 requested) and removed 20 (127 requested) atoms. Cycle 25: After refmac, R = 0.1892 (Rfree = 0.000) for 2958 atoms. Found 65 (259 requested) and removed 14 (129 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.67 1.69 Round 1: 264 peptides, 4 chains. Longest chain 73 peptides. Score 0.956 Round 2: 263 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 3: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 4: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 5: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2927 restraints for refining 2757 atoms. 978 conditional restraints added. Observations/parameters ratio is 3.68 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2068 (Rfree = 0.000) for 2757 atoms. Found 131 (240 requested) and removed 18 (120 requested) atoms. Cycle 27: After refmac, R = 0.2022 (Rfree = 0.000) for 2862 atoms. Found 67 (250 requested) and removed 9 (125 requested) atoms. Cycle 28: After refmac, R = 0.1955 (Rfree = 0.000) for 2915 atoms. Found 68 (255 requested) and removed 6 (127 requested) atoms. Cycle 29: After refmac, R = 0.1918 (Rfree = 0.000) for 2965 atoms. Found 72 (260 requested) and removed 16 (130 requested) atoms. Cycle 30: After refmac, R = 0.1881 (Rfree = 0.000) for 3008 atoms. Found 70 (263 requested) and removed 17 (131 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.67 1.69 Round 1: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 2: 262 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 3: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 4: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 5: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2967 restraints for refining 2807 atoms. 1009 conditional restraints added. Observations/parameters ratio is 3.62 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2069 (Rfree = 0.000) for 2807 atoms. Found 143 (245 requested) and removed 13 (122 requested) atoms. Cycle 32: After refmac, R = 0.2011 (Rfree = 0.000) for 2936 atoms. Found 80 (256 requested) and removed 12 (128 requested) atoms. Cycle 33: After refmac, R = 0.1950 (Rfree = 0.000) for 2992 atoms. Found 57 (262 requested) and removed 11 (131 requested) atoms. Cycle 34: After refmac, R = 0.1910 (Rfree = 0.000) for 3030 atoms. Found 45 (265 requested) and removed 22 (132 requested) atoms. Cycle 35: After refmac, R = 0.1883 (Rfree = 0.000) for 3043 atoms. Found 58 (266 requested) and removed 16 (133 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.67 1.69 Round 1: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 2: 262 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 3: 265 peptides, 5 chains. Longest chain 73 peptides. Score 0.952 Round 4: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Round 5: 262 peptides, 7 chains. Longest chain 73 peptides. Score 0.941 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 2999 restraints for refining 2815 atoms. 1041 conditional restraints added. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2072 (Rfree = 0.000) for 2815 atoms. Found 131 (245 requested) and removed 26 (122 requested) atoms. Cycle 37: After refmac, R = 0.2034 (Rfree = 0.000) for 2909 atoms. Found 71 (255 requested) and removed 7 (127 requested) atoms. Cycle 38: After refmac, R = 0.1977 (Rfree = 0.000) for 2968 atoms. Found 61 (259 requested) and removed 2 (129 requested) atoms. Cycle 39: After refmac, R = 0.1932 (Rfree = 0.000) for 3024 atoms. Found 58 (264 requested) and removed 15 (132 requested) atoms. Cycle 40: After refmac, R = 0.1894 (Rfree = 0.000) for 3056 atoms. Found 54 (267 requested) and removed 21 (133 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.67 1.69 Round 1: 265 peptides, 4 chains. Longest chain 73 peptides. Score 0.957 Round 2: 262 peptides, 5 chains. Longest chain 72 peptides. Score 0.950 Round 3: 263 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 4: 262 peptides, 6 chains. Longest chain 72 peptides. Score 0.946 Round 5: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Taking the results from Round 1 Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 40620 reflections ( 79.26 % complete ) and 3033 restraints for refining 2810 atoms. 1075 conditional restraints added. Observations/parameters ratio is 3.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2100 (Rfree = 0.000) for 2810 atoms. Found 156 (245 requested) and removed 9 (122 requested) atoms. Cycle 42: After refmac, R = 0.2047 (Rfree = 0.000) for 2952 atoms. Found 82 (258 requested) and removed 7 (129 requested) atoms. Cycle 43: After refmac, R = 0.1972 (Rfree = 0.000) for 3017 atoms. Found 70 (264 requested) and removed 14 (132 requested) atoms. Cycle 44: After refmac, R = 0.1921 (Rfree = 0.000) for 3066 atoms. Found 58 (268 requested) and removed 20 (134 requested) atoms. Cycle 45: After refmac, R = 0.1879 (Rfree = 0.000) for 3093 atoms. Found 72 (271 requested) and removed 18 (135 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.66 1.68 Round 1: 262 peptides, 5 chains. Longest chain 73 peptides. Score 0.950 Round 2: 261 peptides, 6 chains. Longest chain 72 peptides. Score 0.945 Round 3: 263 peptides, 6 chains. Longest chain 62 peptides. Score 0.946 Round 4: 263 peptides, 6 chains. Longest chain 73 peptides. Score 0.946 Round 5: 264 peptides, 5 chains. Longest chain 73 peptides. Score 0.951 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 0, Residues 0, Estimated correctness of the model 99.9 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2pr7-1_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 40620 reflections ( 79.26 % complete ) and 3083 restraints for refining 2835 atoms. 1141 conditional restraints added. Observations/parameters ratio is 3.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2134 (Rfree = 0.000) for 2835 atoms. Found 0 (247 requested) and removed 1 (123 requested) atoms. Cycle 47: After refmac, R = 0.2033 (Rfree = 0.000) for 2829 atoms. Found 0 (242 requested) and removed 1 (123 requested) atoms. Cycle 48: After refmac, R = 0.1979 (Rfree = 0.000) for 2824 atoms. Found 0 (237 requested) and removed 0 (123 requested) atoms. Cycle 49: After refmac, R = 0.1941 (Rfree = 0.000) for 2823 atoms. TimeTaking 48.25